From 97002c064b81101eafd6410fab1ad8eddeebce04 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 4 Aug 2025 08:19:38 -0700
Subject: [PATCH 01/61] Gradle 9.0.0 version updates

---
 build.gradle                             | 1 +
 gradle.properties                        | 4 +++-
 gradle/wrapper/gradle-wrapper.properties | 2 +-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/build.gradle b/build.gradle
index 7a6302cc..aad434ae 100644
--- a/build.gradle
+++ b/build.gradle
@@ -30,6 +30,7 @@ repositories {
 dependencies {
     implementation gradleApi()
     implementation localGroovy()
+    implementation "org.apache.groovy:groovy-sql:${groovySqlVersion}"
     api "org.apache.commons:commons-lang3:${commonsLang3Version}"
     api "org.apache.commons:commons-text:${commonsTextVersion}"
     api "commons-io:commons-io:${commonsIoVersion}"
diff --git a/gradle.properties b/gradle.properties
index e02ba1cb..d032ea94 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,6 +1,6 @@
 artifactory_contextUrl=https://labkey.jfrog.io/artifactory
 
-artifactoryPluginVersion=5.2.5
+artifactoryPluginVersion=6.0.0
 
 commonsIoVersion=2.20.0
 commonsLang3Version=3.18.0
@@ -9,6 +9,8 @@ commonsTextVersion=1.14.0
 grgitGradleVersion=5.3.2
 graphqlJavaVersion=24.2
 
+groovySqlVersion=4.0.27
+
 httpclientVersion=5.5
 httpcoreVersion=5.3.4
 
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index d4081da4..2a84e188 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.0.0-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

From 6af9080f49c89f2c390c323a1f068219138e7776 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 4 Aug 2025 08:21:54 -0700
Subject: [PATCH 02/61] white space

---
 .idea/misc.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.idea/misc.xml b/.idea/misc.xml
index 2c6efcb6..5c1ea9b3 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -8,4 +8,4 @@
     <option name="languageLevel" value="ES6" />
   </component>
   <component name="ProjectRootManager" version="2" languageLevel="JDK_17" default="true" project-jdk-name="17" project-jdk-type="JavaSDK" />
-</project>
\ No newline at end of file
+</project>

From 315adc55086e35b83f9a17653a04c820b14dc9af Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 5 Aug 2025 06:57:45 -0700
Subject: [PATCH 03/61] Snapshot version number

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index aad434ae..6a1f907e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -43,7 +43,7 @@ dependencies {
 }
 
 group = 'org.labkey.build'
-project.version = "6.4.0-SNAPSHOT"
+project.version = "6.4.0-gradle9-SNAPSHOT"
 
 gradlePlugin {
     plugins {

From beb8bc16a042c6c9da7f3a29640428bddeeb04ff Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 5 Aug 2025 11:06:22 -0700
Subject: [PATCH 04/61] Configuration cache work for DoThenSetup and DeployApp

---
 README.md                                     |   4 +-
 .../org/labkey/gradle/plugin/Database.groovy  |   3 +
 .../labkey/gradle/plugin/Distribution.groovy  |   3 +-
 .../labkey/gradle/plugin/ServerDeploy.groovy  |   1 +
 .../org/labkey/gradle/plugin/TeamCity.groovy  |   8 +-
 .../labkey/gradle/plugin/TestRunner.groovy    |   6 +-
 .../plugin/extension/TeamCityExtension.groovy |  67 +------
 .../plugin/extension/UiTestExtension.groovy   |   7 +-
 .../org/labkey/gradle/task/Bootstrap.groovy   |   7 +-
 .../org/labkey/gradle/task/DeployApp.groovy   |  10 +-
 .../org/labkey/gradle/task/DoThenSetup.groovy | 181 ++++++++++++------
 .../labkey/gradle/task/InstallRPackage.groovy |   3 +-
 .../labkey/gradle/task/RunTestSuite.groovy    |   3 +-
 .../org/labkey/gradle/task/StartLabKey.groovy |   9 +-
 .../org/labkey/gradle/task/StopLabKey.groovy  |   7 +-
 .../labkey/gradle/task/TeamCityDbSetup.groovy |   5 +-
 .../gradle/task/TeamCityPropertiesTask.groovy | 135 +++++++++++++
 .../org/labkey/gradle/util/BuildUtils.groovy  |  25 ++-
 .../gradle/util/DatabaseProperties.groovy     |  54 +++---
 .../labkey/gradle/util/PropertiesUtils.groovy |  21 +-
 .../org/labkey/gradle/util/SqlUtils.groovy    |  85 --------
 21 files changed, 375 insertions(+), 269 deletions(-)
 create mode 100644 src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
 delete mode 100644 src/main/groovy/org/labkey/gradle/util/SqlUtils.groovy

diff --git a/README.md b/README.md
index 519f8dc0..5b612b14 100644
--- a/README.md
+++ b/README.md
@@ -15,9 +15,11 @@ on how to do that, including how to develop and test locally and the versioning
 
 ### TBD
 *Released*: TBD
-(Earliest compatible LabKeyversion: 25.2)
+(Earliest compatible LabKey version: TBD)
 - Update `PurgeArtifacts` task to be compatible with configuration cache and to work with input files so archived projects can be kept up to date
 - Update dependency versions
+- Update DoThenSetup and its relatives to be compatible with configuration cache
+- Update DeployApp for better configuration cache compatibility
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/plugin/Database.groovy b/src/main/groovy/org/labkey/gradle/plugin/Database.groovy
index 8856b63a..47eb377e 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Database.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Database.groovy
@@ -52,6 +52,7 @@ class Database implements Plugin<Project>
                 task.group = GroupNames.DATABASE
                 task.description = "Switch to SQL Server configuration"
                 task.dbType = "mssql"
+                task.driverFiles.setFrom(project.configurations.driver)
         }
     }
 
@@ -62,6 +63,7 @@ class Database implements Plugin<Project>
                 task.group = GroupNames.DATABASE
                 task.description = "Switch to SQL Server configuration using jTDS driver"
                 task.dbType = "jtds"
+                task.driverFiles.setFrom(project.configurations.driver)
         }
     }
 
@@ -71,6 +73,7 @@ class Database implements Plugin<Project>
             Bootstrap task ->
                 task.group = GroupNames.DATABASE
                 task.description = "Switch to bootstrap database properties as defined in current db.config file"
+                task.driverFiles.setFrom(project.configurations.driver)
         }
     }
 }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy b/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
index a7fe0d96..a00baec4 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
@@ -29,6 +29,7 @@ import org.labkey.gradle.plugin.extension.DistributionExtension
 import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.ModuleDistribution
+import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 import org.labkey.gradle.util.PomFileHelper
@@ -46,7 +47,7 @@ class Distribution implements Plugin<Project>
         // We add the TeamCity extension here if it doesn't exist because we will use the build
         // number property from TeamCity in the distribution artifact names, if present.
         TeamCityExtension teamCityExt  = project.getExtensions().findByType(TeamCityExtension.class)
-        if (TeamCityExtension.isOnTeamCity(project) && teamCityExt == null)
+        if (TeamCityPropertiesTask.isOnTeamCity(project) && teamCityExt == null)
             project.extensions.create("teamCity", TeamCityExtension, project)
 
         if (BuildUtils.getServerProject(project) != null) {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index a99a121b..e309235c 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -195,6 +195,7 @@ class ServerDeploy implements Plugin<Project>
             DoThenSetup task ->
                 task.group = GroupNames.DEPLOY
                 task.description = "Installs application.properties into the tomcat configuration directory. Sets default database properties."
+                task.driverFiles.setFrom(project.configurations.driver)
                 // stage the application first to try to avoid multiple Tomcat restarts
                 task.mustRunAfter(project.tasks.stageApp)
         }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index cc554af7..7c5cf72a 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -33,6 +33,7 @@ import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.PickDb
 import org.labkey.gradle.task.RunTestSuite
 import org.labkey.gradle.task.TeamCityDbSetup
+import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.task.UndeployModules
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
@@ -93,8 +94,8 @@ class TeamCity extends Tomcat
                         spec.classpath {
                             [project.configurations.uiTestRuntimeClasspath, project.tasks.jar]
                         }
-                        spec.systemProperties["labkey.server"] = TeamCityExtension.getLabKeyServer(project)
-                        spec.args = ["set", TeamCityExtension.getLabKeyUsername(project), TeamCityExtension.getLabKeyPassword(project)]
+                        spec.systemProperties["labkey.server"] = TeamCityPropertiesTask.getLabKeyServer(project)
+                        spec.args = ["set", TeamCityPropertiesTask.getLabKeyUsername(project), TeamCityPropertiesTask.getLabKeyPassword(project)]
                     })
                 }
         }
@@ -201,6 +202,7 @@ class TeamCity extends Tomcat
                         task.description = "Copy properties file for running tests for ${shortType}"
                         task.dbType = "${shortType}"
                         task.dbPropertiesChanged = true
+                        task.driverFiles.setFrom(project.configurations.driver)
                 }
                 pickDbTask = project.tasks.named(pickDbTaskName)
             }
@@ -268,7 +270,7 @@ class TeamCity extends Tomcat
                     task.group = GroupNames.TEST_SERVER
                     task.description = "Generate server properties file to run with modules from a specified distribution"
                     task.doLast {
-                        project.logger.info("inheriting from distribution ${inheritedDistPath}")
+                        task.logger.info("inheriting from distribution ${inheritedDistPath}")
                         Set<String> includeModules = new HashSet<>()
                         project.project(inheritedDistPath).configurations.distribution.dependencies.each {
                             includeModules.add(it.getName())
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
index 61b9821c..11d80ef5 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
@@ -17,8 +17,8 @@ package org.labkey.gradle.plugin
 
 import org.gradle.api.Project
 import org.gradle.api.Task
-import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.RunTestSuite
+import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 
@@ -88,7 +88,7 @@ class TestRunner extends UiTest
                         classpath {
                             [project.configurations.uiTestRuntimeClasspath, project.tasks.jar]
                         }
-                        systemProperties["labkey.server"] = TeamCityExtension.getLabKeyServer(project)
+                        systemProperties["labkey.server"] = TeamCityPropertiesTask.getLabKeyServer(project)
                         args = ["set"]
                         standardInput = System.in
                     })
@@ -107,7 +107,7 @@ class TestRunner extends UiTest
                         classpath {
                             [project.configurations.uiTestRuntimeClasspath, project.tasks.jar]
                         }
-                        systemProperties["labkey.server"] = TeamCityExtension.getLabKeyServer(project)
+                        systemProperties["labkey.server"] = TeamCityPropertiesTask.getLabKeyServer(project)
                         args = ["ensure"]
                         standardInput = System.in
                     })
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
index 6e551975..9ee9b7b0 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
@@ -17,6 +17,7 @@ package org.labkey.gradle.plugin.extension
 
 import org.apache.commons.io.FileUtils
 import org.gradle.api.Project
+import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.DatabaseProperties
 
 import java.nio.charset.StandardCharsets
@@ -136,10 +137,6 @@ class TeamCityExtension
         (Boolean) getTeamCityProperty("teamcity.build.branch.is_default", true)
     }
 
-    static boolean isOnTeamCity(Project project)
-    {
-        return project.hasProperty('teamcity')
-    }
 
     String getTeamCityProperty(String name)
     {
@@ -148,68 +145,8 @@ class TeamCityExtension
 
     Object getTeamCityProperty(String name, Object defaultValue)
     {
-        getTeamCityProperty(project, name, defaultValue)
-    }
-
-    static Object getTeamCityProperty(Project project, String name, Object defaultValue)
-    {
-        if (isOnTeamCity(project))
-            return project.teamcity[name] != null ? project.teamcity[name] : defaultValue
-        else if (project.hasProperty(name))
-            return project.property(name)
-        else
-            return defaultValue
-    }
-
-    static Properties getTeamCityProperties(Project project)
-    {
-        if (isOnTeamCity(project))
-        {
-            def tcProps = new Properties()
-            tcProps.putAll(project.teamcity)
-            return tcProps
-        }
-        else
-            return new Properties()
-    }
-
-    static String getLabKeyServer(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.server", "http://localhost")
-    }
-
-    static String getLabKeyContextPath(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.contextpath", null)
+        TeamCityPropertiesTask.getTeamCityProperty(project, name, defaultValue)
     }
 
-    static String getLabKeyServerPort(Project project)
-    {
-        return getTeamCityProperty(project, 'tomcat.port', null)
-    }
-
-    static String getLabKeyServerShutdownPort(Project project)
-    {
-        return getTeamCityProperty(project, 'tomcat.shutdown', null)
-    }
-
-    static String getLabKeyServerKeystore(Project project)
-    {
-        return getTeamCityProperty(project, 'labkey.keystore', null)
-    }
 
-    static String getLabKeyServerKeystorePassword(Project project)
-    {
-        return getTeamCityProperty(project, 'labkey.keystore.password', null)
-    }
-
-    static String getLabKeyUsername(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.server.email", "teamcity@labkey.test")
-    }
-
-    static String getLabKeyPassword(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.server.password", "We'reSo\$tr0ng@yekbal1!")
-    }
 }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy
index a38aa248..2d38a9e4 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy
@@ -18,6 +18,7 @@ package org.labkey.gradle.plugin.extension
 
 import org.gradle.api.GradleException
 import org.gradle.api.Project
+import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.PropertiesUtils
@@ -35,7 +36,7 @@ class UiTestExtension
     {
         this.project = project
         TeamCityExtension tcExtension = project.extensions.findByType(TeamCityExtension.class)
-        if (TeamCityExtension.isOnTeamCity(project) && tcExtension == null)
+        if (TeamCityPropertiesTask.isOnTeamCity(project) && tcExtension == null)
             this.tcExtension = project.extensions.create("teamCity", TeamCityExtension, project)
     }
 
@@ -72,7 +73,7 @@ class UiTestExtension
         else if (DatabaseProperties.getPickedConfigFile(project).exists())
         {
             project.logger.info("Found config file ${DatabaseProperties.getPickedConfigFile(project).getAbsolutePath()} to get db properties from")
-            DatabaseProperties dbProperties = new DatabaseProperties(project, false)
+            DatabaseProperties dbProperties = new DatabaseProperties(project.path, DatabaseProperties.getPickedConfigFile(project), false)
             // read database configuration, but don't include jdbcUrl and other non-"database"
             // properties because they "cause problems" (quote from the test/build.xml file)
             for (String name : dbProperties.getConfigProperties().stringPropertyNames())
@@ -86,7 +87,7 @@ class UiTestExtension
         if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null)
         {
             def propertiesFile = project.project(BuildUtils.getTestProjectPath(project.gradle)).file(propertiesFileName)
-            if (TeamCityExtension.isOnTeamCity(project))
+            if (TeamCityPropertiesTask.isOnTeamCity(project))
             {
                 // Load properties from template when running on TeamCity.
                 // These properties control which TeamCity properties are loaded by `RunTestSuite.setTeamCityProperties`
diff --git a/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy b/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
index b9d967f4..31c01006 100644
--- a/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
@@ -16,9 +16,8 @@
 package org.labkey.gradle.task
 
 import org.labkey.gradle.util.DatabaseProperties
-import org.labkey.gradle.util.SqlUtils
 
-class Bootstrap extends DoThenSetup
+abstract class Bootstrap extends DoThenSetup
 {
     boolean dbPropertiesChanged = true
 
@@ -27,13 +26,13 @@ class Bootstrap extends DoThenSetup
     {
         setDatabaseProperties()
 
-        SqlUtils.dropDatabase(this.project, databaseProperties)
+        dropDatabase(getPath(), databaseProperties)
         databaseProperties.interpolateCompositeProperties()
     }
 
     @Override
     protected void setDatabaseProperties()
     {
-        databaseProperties = new DatabaseProperties(project, true)
+        databaseProperties = new DatabaseProperties(getPath(), chosenPropsFile.get().asFile, true)
     }
 }
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
index 2506c12c..a0f0a5ab 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
@@ -18,6 +18,8 @@ package org.labkey.gradle.task
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputDirectory
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
@@ -45,13 +47,19 @@ abstract class DeployApp extends DeployAppBase
     @OutputDirectory
     final abstract DirectoryProperty deployBinDir = BuildUtils.getRootBuildDirectoryProperty(project, ServerDeploy.DEPLOY_BIN_DIR)
 
+    @Input
+    final abstract Property<Boolean> useLocalBuild = project.objects.property(Boolean).convention(project.hasProperty("useLocalBuild") && "false" != project.property("useLocalBuild"))
+
+    @InputDirectory
+    File restartTriggerFileDir = BuildUtils.getTriggerFileDir(project)
+
     @TaskAction
     void action()
     {
         deployModules()
         deployPipelineJars()
         deployPlatformBinaries(deployBinDir.get().asFile)
-        BuildUtils.updateRestartTriggerFile(project)
+        BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFileDir)
     }
 
     private void deployModules()
diff --git a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
index 51799759..71c3a71a 100644
--- a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
@@ -15,32 +15,69 @@
  */
 package org.labkey.gradle.task
 
-import org.gradle.api.DefaultTask
-import org.gradle.api.Project
+import groovy.sql.Sql
+import org.gradle.api.GradleException
+import org.gradle.api.file.ConfigurableFileCollection
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DuplicatesStrategy
+import org.gradle.api.file.FileSystemOperations
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.InputFile
+import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.TaskAction
-import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.PropertiesUtils
 
-import java.util.function.Function
+import javax.inject.Inject
+import java.sql.Driver
+import java.sql.DriverManager
 
 // TODO making this extend from RestartTriggerTask causes the following error on TeamCity:
 //  Cannot fingerprint input property 'databaseProperties': value 'org.labkey.gradle.util.DatabaseProperties@286cb41a' cannot be serialized.
 // Even though RestartTriggerTask has nothing to do with the `databaseProperties`
-class DoThenSetup extends DefaultTask
+abstract class DoThenSetup extends TeamCityPropertiesTask
 {
     // TODO rethink this input declaration. Dependence on a file makes more sense
     @Optional @Input
     protected DatabaseProperties databaseProperties
 
+    @InputFiles
+    abstract ConfigurableFileCollection getDriverFiles()
+
     @Input
     boolean dbPropertiesChanged = false
 
+    @InputFile
+    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
+
+    @InputFile
+    final abstract RegularFileProperty applicationPropsFile = project.objects.fileProperty().fileValue(new File(BuildUtils.getEmbeddedConfigPath(project), "application.properties"))
+
+    @Input
+    final abstract Property<Boolean> useSsl = project.objects.property(Boolean).convention(project.hasProperty("useSsl"))
+    @Input
+    final abstract Property<String> portNumber = project.objects.property(String).convention(project.hasProperty("useSsl") ? "8443" : "8080")
+    @Input
+    final abstract Property<Boolean> useLocalBuild = project.objects.property(Boolean).convention(project.hasProperty("useLocalBuild") && "false" != project.property("useLocalBuild"))
+
+    @Input // in .properties files, backward slashes are seen as escape characters, so all paths must use forward slashes, even on Windows
+    final abstract Property<String> pathToServer = project.objects.property(String).convention(project.rootDir.getAbsolutePath().replaceAll("\\\\", "/"))
+
+    @Input
+    final abstract Property<String> embeddedDir = project.objects.property(String).convention(BuildUtils.getEmbeddedConfigPath(project))
+    @InputDirectory
+    File configsDir = new File(BuildUtils.getConfigsProject(project).projectDir, "configs")
+
+    @InputDirectory
+    File restartTriggerFileDir = BuildUtils.getTriggerFileDir(project)
+
+    @Inject abstract FileSystemOperations getFs()
+
     protected void doDatabaseTask()
     {
         setDatabaseProperties()
@@ -52,50 +89,27 @@ class DoThenSetup extends DefaultTask
         if (!embeddedConfigUpToDate()) {
             Properties configProperties = databaseProperties.getConfigProperties()
             configProperties.putAll(getExtraJdbcProperties())
-            // in .properties files, backward slashes are seen as escape characters, so all paths must use forward slashes, even on Windows
-            configProperties.setProperty("pathToServer", project.rootDir.getAbsolutePath().replaceAll("\\\\", "/"))
-
-            configProperties.setProperty("serverPort", tcPropOrDefault(project,
-                    TeamCityExtension::getLabKeyServerPort,
-                    "serverPort",
-                    project.hasProperty("useSsl") ? "8443" : "8080"))
-
-            configProperties.setProperty("contextPath", tcPropOrDefault(project,
-                    TeamCityExtension::getLabKeyContextPath,
-                    "contextPath",
-                    ""))
-
-            configProperties.setProperty("shutdownPort", tcPropOrDefault(project,
-                    TeamCityExtension::getLabKeyServerShutdownPort,
-                    "shutdownPort",
-                    "8081"))
-
-            if (project.hasProperty("useSsl")) {
-                configProperties.setProperty("keyStore", tcPropOrDefault(project,
-                        TeamCityExtension::getLabKeyServerKeystore,
-                        "keyStore",
-                        "/opt/teamcity-agent/localhost.keystore"))
-
-                configProperties.setProperty("keyStorePassword", tcPropOrDefault(project,
-                        TeamCityExtension::getLabKeyServerKeystorePassword,
-                        "keyStorePassword",
-                        "changeit"))
+            configProperties.setProperty("pathToServer", pathToServer.get())
+            configProperties.setProperty("serverPort", labKeyServerPort.get())
+            configProperties.setProperty("contextPath", contextPath.get())
+            configProperties.setProperty("shutdownPort", shutdownPort.get())
+            if (useSsl.get()) {
+                configProperties.setProperty("keyStore", keyStore.get())
+                configProperties.setProperty("keyStorePassword", keyStorePassword.get())
             }
 
-            String embeddedDir = BuildUtils.getEmbeddedConfigPath(project)
-            File configsDir = new File(BuildUtils.getConfigsProject(project).projectDir, "configs")
-            project.copy({ CopySpec copy ->
+            fs.copy({ CopySpec copy ->
                 copy.from configsDir
-                copy.into embeddedDir
+                copy.into embeddedDir.get()
                 copy.include "application.properties"
                 copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
                 copy.filter({ String line ->
                     // Always uncomment properties prepended by '#setupTask#'
                     line = line.replace("#setupTask#", "")
-                    if (project.hasProperty("useSsl")) {
+                    if (useSsl.get()) {
                         line = line.replace("#server.ssl", "server.ssl")
                     }
-                    if (project.hasProperty("useLocalBuild") && "false" != project.property("useLocalBuild")) {
+                    if (useLocalBuild.get()) {
                         // Enable properties that require 'useLocalBuild' (e.g. 'context.webAppLocation' and 'spring.devtools.restart.additional-paths')
                         line = line.replace("#useLocalBuild#", "")
                     }
@@ -117,7 +131,7 @@ class DoThenSetup extends DefaultTask
                     return PropertiesUtils.replaceProps(line, configProperties, false)
                 })
             })
-            BuildUtils.updateRestartTriggerFile(project)
+            BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFileDir)
         }
     }
 
@@ -125,10 +139,11 @@ class DoThenSetup extends DefaultTask
      * Get 'extraJdbc*' properties from TeamCity.
      * Used as string replacements when deploying 'labkey.xml' and 'application.properties'
      */
-    private Properties getExtraJdbcProperties()
+    @Input
+    Properties getExtraJdbcProperties()
     {
         def extraJdbcProperties = new Properties()
-        def tcProperties = TeamCityExtension.getTeamCityProperties(project)
+        def tcProperties = isOnTeamCity.get() ? getTeamCityProperties(project) : new Properties()
         for (Map.Entry entry : tcProperties.entrySet())
         {
             if (entry.getKey().startsWith("extraJdbc"))
@@ -144,11 +159,11 @@ class DoThenSetup extends DefaultTask
         if (this.dbPropertiesChanged)
             return false
 
-        File dbPropFile = DatabaseProperties.getPickedConfigFile(project)
-        File applicationPropsFile = new File(BuildUtils.getEmbeddedConfigPath(project), "application.properties")
-        if (!dbPropFile.exists() || !applicationPropsFile.exists())
+        File dbPropFile = chosenPropsFile.get().getAsFile()
+        File _applicationPropsFile = applicationPropsFile.get().getAsFile()
+        if (!dbPropFile.exists() || !_applicationPropsFile.exists())
             return false
-        if (dbPropFile.lastModified() < applicationPropsFile.lastModified())
+        if (dbPropFile.lastModified() < _applicationPropsFile.lastModified())
         {
             return true
         }
@@ -157,7 +172,7 @@ class DoThenSetup extends DefaultTask
 
     protected void setDatabaseProperties()
     {
-        databaseProperties = new DatabaseProperties(project, false)
+        databaseProperties = new DatabaseProperties(getPath(), chosenPropsFile.get().asFile, false)
     }
 
     void setDatabaseProperties(DatabaseProperties dbProperties)
@@ -170,15 +185,71 @@ class DoThenSetup extends DefaultTask
         return databaseProperties
     }
 
-    private static String tcPropOrDefault(Project project, Function<Project, String> tcPropertyFunc, String projectPropertyName, String defaultValue)
+
+
+    void execSql(DatabaseProperties params, String sql)
+    {
+        params.interpolateCompositeProperties()
+        String url = params.getJdbcURL()
+        String user = params.getJdbcUser()
+        String password = params.getJdbcPassword()
+        String driverClassName = params.getJdbcDriverClassName()
+        logger.info("in execSql: url ${url} driverClassName ${driverClassName}")
+        logger.debug(" user ${user} password ${password}")
+
+        var loader = GroovyObject.class.classLoader
+        // N.B. It seems like this modification of the loader classpath should not be necessary (or possible) and we
+        // should be able to declare the dependencies on the driver jars in the buildscript { dependencies { } } block,
+        // but see this (admittedly old) post https://discuss.gradle.org/t/class-pathes-in-gradle-script/16655, which
+        // has a response that explains that "the caller to Sql isn't actually the build script, it is Groovy. So,
+        // you need to load the driver in the same classloader as Groovy." Maybe we'd have a different story if we
+        // were using Java instead of Groovy. Someday.
+        getDriverFiles().each {File file ->
+            logger.info("adding classLoader URL " + file.toURI().toURL())
+            loader.addURL(file.toURI().toURL())
+        }
+        Class driverClass = loader.loadClass(driverClassName)
+        logger.info("driverClass is ${driverClass}")
+
+        Driver driverInstance = (Driver) driverClass.newInstance()
+        DriverManager.registerDriver(driverInstance)
+
+        Sql db = null
+        try
+        {
+            db = Sql.newInstance(url, user, password)
+            db.execute(sql)
+        }
+        catch (Exception e)
+        {
+            logger.error(e.toString())
+        }
+        finally
+        {
+            if (db != null)
+                db.close()
+        }
+    }
+
+    void dropDatabase(String projectPath, DatabaseProperties dbProperties)
     {
-        String value = tcPropertyFunc.apply(project)
-        if (value == null) {
-            if (project.hasProperty(projectPropertyName))
-                value = (String) project.property(projectPropertyName)
-            else
-                value = defaultValue
+        Properties properties = dbProperties.getConfigProperties()
+        logger.info("in dropDatabase for ${projectPath}, properties are ${properties}")
+        String toDrop = dbProperties.getJdbcDatabase()
+        if (toDrop == null || toDrop.equals("labkey"))
+        {
+            throw new GradleException("Must specify a database that is not 'labkey'")
+        }
+        else
+        {
+            DatabaseProperties dropProps = new DatabaseProperties(projectPath, dbProperties)
+            // need to connect to the built-in default database in order to drop the database
+            dropProps.setJdbcDatabase(dbProperties.getDefaultDatabase())
+            dropProps.setJdbcUrlParams("")
+
+            logger.info("Attempting to drop database ${toDrop}")
+            execSql(dropProps, "DROP DATABASE \"${toDrop}\";")
         }
-        return value
     }
+
 }
diff --git a/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy b/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy
index f3674b67..c5eb4f0a 100644
--- a/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy
@@ -22,7 +22,6 @@ import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
-import org.labkey.gradle.plugin.extension.TeamCityExtension
 
 class InstallRPackage extends DefaultTask
 {
@@ -138,7 +137,7 @@ class InstallRPackage extends DefaultTask
 
     static String getRLibsUserPath(Project project)
     {
-        return TeamCityExtension.getTeamCityProperty(project, "R_LIBS_USER", System.getenv("R_LIBS_USER"))
+        return TeamCityPropertiesTask.getTeamCityProperty(project, "R_LIBS_USER", System.getenv("R_LIBS_USER"))
     }
 
     void installRPackage(String scriptName)
diff --git a/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy b/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy
index 9d259663..6c74e78a 100644
--- a/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy
@@ -18,7 +18,6 @@ package org.labkey.gradle.task
 import org.apache.commons.lang3.StringUtils
 import org.gradle.api.tasks.Internal
 import org.labkey.gradle.plugin.TeamCity
-import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.util.DatabaseProperties
 
 /**
@@ -50,7 +49,7 @@ abstract class RunTestSuite extends RunUiTest
 
     protected void setTeamCityProperties()
     {
-        if (TeamCityExtension.isOnTeamCity(project))
+        if (TeamCityPropertiesTask.isOnTeamCity(project))
         {
             systemProperty "teamcity.tests.recentlyFailedTests.file", project.teamcity['teamcity.tests.recentlyFailedTests.file']
             systemProperty "teamcity.build.changedFiles.file", project.teamcity['teamcity.build.changedFiles.file']
diff --git a/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy b/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
index 680c59be..aa0e7a70 100644
--- a/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
@@ -24,7 +24,6 @@ import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.Tomcat
 import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
-import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.util.BuildUtils
 
 import java.util.stream.Collectors
@@ -51,7 +50,7 @@ class StartLabKey extends DefaultTask
         }
         else
         {
-            String javaHome = TeamCityExtension.getTeamCityProperty(project, "tomcatJavaHome", System.getenv("JAVA_HOME"))
+            String javaHome = TeamCityPropertiesTask.getTeamCityProperty(project, "tomcatJavaHome", System.getenv("JAVA_HOME"))
             if (StringUtils.isEmpty(javaHome))
                 throw new GradleException("JAVA_HOME must be set in order to start your embedded tomcat server.")
             File javaBin = new File(javaHome, "bin")
@@ -87,7 +86,7 @@ class StartLabKey extends DefaultTask
         optsList.add(project.tomcat.assertionFlag)
         optsList.add("-Ddevmode=${LabKeyExtension.isDevMode(project)}".toString())
         optsList.addAll(project.tomcat.catalinaOpts.split(" "))
-        optsList.add("-Xmx${TeamCityExtension.getTeamCityProperty(project, "Xmx", project.tomcat.maxMemory)}".toString())
+        optsList.add("-Xmx${TeamCityPropertiesTask.getTeamCityProperty(project, "Xmx", project.tomcat.maxMemory)}".toString())
         if (project.tomcat.disableRecompileJsp)
             optsList.add("-Dlabkey.disableRecompileJsp=true")
         if (project.tomcat.ignoreModuleSource)
@@ -95,9 +94,9 @@ class StartLabKey extends DefaultTask
         optsList.add(project.tomcat.trustStore)
         optsList.add(project.tomcat.trustStorePassword)
 
-        if (TeamCityExtension.isOnTeamCity(project) && SystemUtils.IS_OS_UNIX)
+        if (TeamCityPropertiesTask.isOnTeamCity(project) && SystemUtils.IS_OS_UNIX)
         {
-            optsList.add("-DsequencePipelineEnabled=${TeamCityExtension.getTeamCityProperty(project, "sequencePipelineEnabled", false)}".toString())
+            optsList.add("-DsequencePipelineEnabled=${TeamCityPropertiesTask.getTeamCityProperty(project, "sequencePipelineEnabled", false)}".toString())
         }
 
         if (project.hasProperty("extraCatalinaOpts"))
diff --git a/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy b/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
index 2821e334..1263c6c0 100644
--- a/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
@@ -16,18 +16,23 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.util.PropertiesUtils
+import org.labkey.gradle.util.BuildUtils
 
 /**
  * Task for stopping a running LabKey instance
  */
 class StopLabKey extends DefaultTask
 {
+    @InputFile
+    File propertiesFile = BuildUtils.getApplicationPropertiesFile(project)
+
     @TaskAction
     void action()
     {
-        def applicationProperties = PropertiesUtils.getApplicationProperties(project)
+        def applicationProperties = PropertiesUtils.getApplicationProperties(propertiesFile)
         def port = applicationProperties.getProperty("management.server.port", applicationProperties.getProperty("server.port"))
         def endpoint =  "${project.hasProperty("useSsl") ? "https" : "http"}://localhost:$port/actuator/shutdown"
         def command = "curl -X POST $endpoint"
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
index 5fc7f349..25ac4009 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
@@ -16,9 +16,8 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.tasks.Input
-import org.labkey.gradle.util.SqlUtils
 
-class TeamCityDbSetup extends DoThenSetup
+abstract class TeamCityDbSetup extends DoThenSetup
 {
     boolean dbPropertiesChanged = true
     @Input
@@ -35,7 +34,7 @@ class TeamCityDbSetup extends DoThenSetup
                 logger.info("The 'testValidationOnly' flag is true, not going to drop the database.")
             }
             else {
-                SqlUtils.dropDatabase(project, databaseProperties)
+                dropDatabase(getPath(), databaseProperties)
             }
         }
         databaseProperties.interpolateCompositeProperties()
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
new file mode 100644
index 00000000..4edaf05d
--- /dev/null
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
@@ -0,0 +1,135 @@
+package org.labkey.gradle.task
+
+import org.gradle.api.DefaultTask
+import org.gradle.api.Project
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.Optional
+
+import java.util.function.Function
+
+abstract class TeamCityPropertiesTask extends DefaultTask
+{
+    @Input
+    final abstract Property<Boolean> useSsl = project.objects.property(Boolean).convention(project.hasProperty("useSsl"))
+
+    @Optional @Input
+    final abstract Property<Boolean> isOnTeamCity = project.objects.property(Boolean).convention(project.hasProperty("teamCity"))
+
+    @Optional @Input
+    final abstract Property<String> labKeyServerPort = project.objects.property(String).convention(
+            tcPropOrDefault(project,
+                    TeamCityPropertiesTask::getLabKeyServerPort,
+                "serverPort", project.hasProperty("useSsl") ? "8443" : "8080"))
+
+    @Optional @Input
+    final abstract Property<String> contextPath = project.objects.property(String).convention(
+            tcPropOrDefault(project,
+                    TeamCityPropertiesTask::getLabKeyContextPath,
+                    "contextPath",
+                    ""))
+
+    @Optional @Input
+    final abstract Property<String> shutdownPort = project.objects.property(String).convention(
+            tcPropOrDefault(project,
+                    TeamCityPropertiesTask::getLabKeyServerShutdownPort,
+                    "shutdownPort",
+                    "8081"))
+    @Optional @Input
+    final abstract Property<String> keyStore = project.objects.property(String).convention(
+            tcPropOrDefault(project,
+                    TeamCityPropertiesTask::getLabKeyServerKeystore,
+                    "keyStore",
+                    "/opt/teamcity-agent/localhost.keystore"))
+
+    @Optional @Input
+    final abstract Property<String> keyStorePassword = project.objects.property(String).convention(
+            tcPropOrDefault(project,
+                    TeamCityPropertiesTask::getLabKeyServerKeystorePassword,
+                    "keyStorePassword",
+                    "changeit"))
+
+    @Optional @Input
+    final abstract Property<String> labKeyServer = project.objects.property(String).convention(getLabKeyServer(project))
+
+
+
+    protected static String tcPropOrDefault(Project project, Function<Project, String> tcPropertyFunc, String projectPropertyName, String defaultValue)
+    {
+        String value = tcPropertyFunc.apply(project)
+        if (value == null) {
+            if (project.hasProperty(projectPropertyName))
+                value = (String) project.property(projectPropertyName)
+            else
+                value = defaultValue
+        }
+        return value
+    }
+
+    static boolean isOnTeamCity(Project project)
+    {
+        return project.hasProperty('teamcity')
+    }
+
+    static Object getTeamCityProperty(Project project, String name, Object defaultValue)
+    {
+        if (isOnTeamCity(project))
+            return project.teamcity[name] != null ? project.teamcity[name] : defaultValue
+        else if (project.hasProperty(name))
+            return project.property(name)
+        else
+            return defaultValue
+    }
+
+    static Properties getTeamCityProperties(Project project)
+    {
+        if (isOnTeamCity(project))
+        {
+            def tcProps = new Properties()
+            tcProps.putAll(project.teamcity)
+            return tcProps
+        }
+        else
+            return new Properties()
+    }
+
+    static String getLabKeyServer(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.server", "http://localhost")
+    }
+
+    static String getLabKeyContextPath(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.contextpath", null)
+    }
+
+    static String getLabKeyServerPort(Project project)
+    {
+        return getTeamCityProperty(project, 'tomcat.port', null)
+    }
+
+    static String getLabKeyServerShutdownPort(Project project)
+    {
+        return getTeamCityProperty(project, 'tomcat.shutdown', null)
+    }
+
+    static String getLabKeyServerKeystore(Project project)
+    {
+        return getTeamCityProperty(project, 'labkey.keystore', null)
+    }
+
+    static String getLabKeyServerKeystorePassword(Project project)
+    {
+        return getTeamCityProperty(project, 'labkey.keystore.password', null)
+    }
+
+    static String getLabKeyUsername(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.server.email", "teamcity@labkey.test")
+    }
+
+    static String getLabKeyPassword(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.server.password", "We'reSo\$tr0ng@yekbal1!")
+    }
+}
diff --git a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
index 4878ebae..c441af9b 100644
--- a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
@@ -33,6 +33,7 @@ import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.plugin.extension.ModuleExtension
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
+import org.labkey.gradle.task.TeamCityPropertiesTask
 
 import java.nio.charset.StandardCharsets
 import java.nio.file.Files
@@ -261,7 +262,7 @@ class BuildUtils
         if (!project.projectDir.exists() && project.hasProperty("downloadLabKeyModules"))
             reasons.add("Project directory ${project.projectDir} does not exist.")
         String propValue = project.hasProperty(property) ? project.property(property) : null
-        String value = TeamCityExtension.getTeamCityProperty(project, property, propValue)
+        String value = TeamCityPropertiesTask.getTeamCityProperty(project, property, propValue)
         if (value == null)
         {
             reasons.add("Project does not have ${property} property")
@@ -491,8 +492,8 @@ class BuildUtils
     static Properties getStandardVCSProperties(project)
     {
         String buildNumber =
-                (String) TeamCityExtension.getTeamCityProperty(project, "system.teamcity.agent.dotnet.build_id", // Unique build ID
-                        TeamCityExtension.getTeamCityProperty(project,"build.number", null))
+                (String) TeamCityPropertiesTask.getTeamCityProperty(project, "system.teamcity.agent.dotnet.build_id", // Unique build ID
+                        TeamCityPropertiesTask.getTeamCityProperty(project,"build.number", null))
         Properties ret = new Properties()
         if (project.plugins.hasPlugin("org.labkey.versioning"))
         {
@@ -885,10 +886,19 @@ class BuildUtils
      */
     static void updateRestartTriggerFile(Project project)
     {
-        if (!project.hasProperty('useLocalBuild') || "false" == project.property("useLocalBuild"))
+        updateRestartTriggerFile(project.hasProperty('useLocalBuild') && "false" != project.property("useLocalBuild"), getTriggerFileDir(project))
+    }
+
+    static File getTriggerFileDir(Project project)
+    {
+        return project.rootProject.layout.buildDirectory.file("deploy/modules").get().getAsFile()
+    }
+
+    static void updateRestartTriggerFile(boolean useLocalBuild, File triggerFileDir)
+    {
+        if (!useLocalBuild)
             return
 
-        File triggerFileDir = project.rootProject.layout.buildDirectory.file("deploy/modules").get().getAsFile()
         if (!triggerFileDir.exists())
             return
 
@@ -954,6 +964,11 @@ class BuildUtils
         return project.rootProject.layout.buildDirectory.get().asFile.path
     }
 
+    static File getApplicationPropertiesFile(Project project)
+    {
+        return new File(getEmbeddedConfigPath(project), "application.properties")
+    }
+
     static Provider<Directory> getRootBuildDirectoryProvider(Project project, String directoryPath)
     {
         return project.rootProject.layout.buildDirectory.dir(directoryPath)
diff --git a/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy b/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
index 47ed91a9..03e37b82 100644
--- a/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
@@ -16,9 +16,12 @@
 package org.labkey.gradle.util
 
 import org.gradle.api.Project
+import org.slf4j.Logger
+import org.slf4j.LoggerFactory
 
 class DatabaseProperties
 {
+    Logger logger = LoggerFactory.getLogger(DatabaseProperties.class)
     private static final String PICKED_DATABASE_CONFIG_FILE = "config.properties"
 
     private static final String JDBC_DRIVER_CLASS_NAME_PROP = "jdbcDriverClassName"
@@ -39,7 +42,7 @@ class DatabaseProperties
     String version // database version, e.g. 9.2
 
     Properties configProperties
-    transient private Project _project
+    String projectPath
 
     DatabaseProperties(String dbTypeAndVersion, String shortType, version)
     {
@@ -49,10 +52,10 @@ class DatabaseProperties
         this.configProperties = new Properties()
     }
 
-    DatabaseProperties(Project project, Boolean useBootstrap)
+    DatabaseProperties(String projectPath, File configFile, Boolean useBootstrap)
     {
-        this._project = project
-        this.configProperties = readDatabaseProperties(project)
+        this.projectPath = projectPath
+        this.configProperties = readDatabaseProperties(configFile, logger)
         if (!this.configProperties.isEmpty())
         {
             setDefaultJdbcProperties(useBootstrap)
@@ -61,9 +64,9 @@ class DatabaseProperties
         }
     }
 
-    DatabaseProperties(Project project, DatabaseProperties copyProperties)
+    DatabaseProperties(String projectPath, DatabaseProperties copyProperties)
     {
-        this._project = project
+        this.projectPath = projectPath
         this.configProperties = (Properties) copyProperties.configProperties.clone()
         this.dbTypeAndVersion = copyProperties.dbTypeAndVersion
         this.shortType = copyProperties.shortType
@@ -80,11 +83,6 @@ class DatabaseProperties
         return BuildUtils.getConfigsProject(project).file(dbConfigFile)
     }
 
-    void setProject(Project project)
-    {
-        this._project = project
-    }
-
     String getJdbcDriverClassName()
     {
         return this.configProperties.get(JDBC_DRIVER_CLASS_NAME_PROP)
@@ -190,19 +188,19 @@ class DatabaseProperties
             return (String) this.configProperties.get(property)
         else
         {
-            _project.logger.info("Default database config property ${property} not defined; returning '${defaultValue}'.")
+            logger.info("Default database config property ${property} not defined; returning '${defaultValue}'.")
             return defaultValue
         }
     }
 
     void interpolateCompositeProperties()
     {
-        this.configProperties.setProperty(JDBC_URL_PROP, PropertiesUtils.parseCompositeProp(_project, this.configProperties, this.configProperties.getProperty(JDBC_URL_PROP)))
+        this.configProperties.setProperty(JDBC_URL_PROP, PropertiesUtils.parseCompositeProp(projectPath, this.configProperties, this.configProperties.getProperty(JDBC_URL_PROP), logger))
     }
 
     void mergePropertiesFromFile()
     {
-        Properties fileProperties = readDatabaseProperties(_project)
+        Properties fileProperties = readDatabaseProperties(BuildUtils.getConfigsProject(project).file(PICKED_DATABASE_CONFIG_FILE), logger)
         for (String name : fileProperties.propertyNames())
         {
             if (this.configProperties.getProperty(name) == null)
@@ -213,28 +211,36 @@ class DatabaseProperties
         setDefaultJdbcProperties(false)
     }
 
-    void writeDbProps()
+    void mergePropertiesFromFile(File file, Logger logger)
     {
-        writeDatabaseProperty(_project, JDBC_URL_PROP, PropertiesUtils.parseCompositeProp(_project, this.configProperties, this.configProperties.getProperty(JDBC_URL_PROP)))
-        writeDatabaseProperty(_project, JDBC_USER_PROP, getJdbcUser())
-        writeDatabaseProperty(_project, JDBC_PASSWORD_PROP, getJdbcPassword())
+        Properties fileProperties = readDatabaseProperties(file, logger)
+        for (String name : fileProperties.propertyNames())
+        {
+            if (this.configProperties.getProperty(name) == null)
+            {
+                this.configProperties.setProperty(name, fileProperties.getProperty(name))
+            }
+        }
+        setDefaultJdbcProperties(false)
     }
 
-    static Properties readDatabaseProperties(Project project)
+    void writeDbProps()
     {
-        return _readDatabaseProperties(project, PICKED_DATABASE_CONFIG_FILE)
+        writeDatabaseProperty(_project, JDBC_URL_PROP, PropertiesUtils.parseCompositeProp(projectPath, this.configProperties, this.configProperties.getProperty(JDBC_URL_PROP), logger))
+        writeDatabaseProperty(_project, JDBC_USER_PROP, getJdbcUser())
+        writeDatabaseProperty(_project, JDBC_PASSWORD_PROP, getJdbcPassword())
     }
 
-    private static Properties _readDatabaseProperties(Project project, String configFile)
+    static Properties readDatabaseProperties(File configFile, Logger logger)
     {
-        if (getConfigFile(project, configFile).exists())
+        if (configFile.exists())
         {
-            Properties props = PropertiesUtils.readFileProperties(BuildUtils.getConfigsProject(project), configFile)
+            Properties props = PropertiesUtils.readFileProperties(configFile)
             return props
         }
         else
         {
-            project.logger.info("No file ${configFile} found.  Returning empty properties.")
+            logger.info("No file ${configFile} found.  Returning empty properties.")
             return new Properties()
         }
     }
diff --git a/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy b/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy
index c1dacbea..d1104ea4 100644
--- a/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy
@@ -17,6 +17,7 @@ package org.labkey.gradle.util
 
 import org.apache.commons.text.StringEscapeUtils
 import org.gradle.api.Project
+import org.slf4j.Logger
 
 import java.util.regex.Matcher
 import java.util.regex.Pattern
@@ -37,12 +38,20 @@ class PropertiesUtils
         return props
     }
 
-    static String parseCompositeProp(Project project, Properties props, String prop)
+    static Properties readFileProperties(File propFile)
+    {
+        Properties props = new Properties()
+        if (propFile.exists())
+            props.load(new FileInputStream(propFile))
+        return props
+    }
+
+    static String parseCompositeProp(String projectPath, Properties props, String prop, Logger logger)
     {
         if (props == null)
-            project.logger.error("${project.path} Properties is null")
+            logger.error("${projectPath} Properties is null")
         else if (prop == null)
-            project.logger.error("${project.path} Property is null; no parsing possible")
+            logger.error("${projectPath} Property is null; no parsing possible")
         else
         {
             Matcher valMatcher = VALUE_PATTERN.matcher(prop)
@@ -52,7 +61,7 @@ class PropertiesUtils
                 if (props.getProperty(p) != null)
                     prop = prop.replace(valMatcher.group(1), (String) (props.getProperty(p)))
                 else
-                    project.logger.error("Unable to find value for ${p} in ${props}")
+                    logger.error("Unable to find value for ${p} in ${props}")
             }
         }
         return prop
@@ -107,10 +116,10 @@ class PropertiesUtils
         }
     }
 
-    static Properties getApplicationProperties(Project project)
+    static Properties getApplicationProperties(File propertiesFile)
     {
         def applicationProperties = new Properties()
-        readProperties(new File(BuildUtils.getEmbeddedConfigPath(project), "application.properties"), applicationProperties)
+        readProperties(propertiesFile, applicationProperties)
         return applicationProperties
     }
 }
diff --git a/src/main/groovy/org/labkey/gradle/util/SqlUtils.groovy b/src/main/groovy/org/labkey/gradle/util/SqlUtils.groovy
deleted file mode 100644
index 6f3d7dfd..00000000
--- a/src/main/groovy/org/labkey/gradle/util/SqlUtils.groovy
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * Copyright (c) 2016-2017 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.gradle.util
-
-import groovy.sql.Sql
-import org.gradle.api.GradleException
-import org.gradle.api.Project
-
-import java.sql.Driver
-import java.sql.DriverManager
-
-class SqlUtils
-{
-    static void execSql(Project project, DatabaseProperties params, String sql)
-    {
-        params.interpolateCompositeProperties()
-        String url = params.getJdbcURL()
-        String user = params.getJdbcUser()
-        String password = params.getJdbcPassword()
-        String driverClassName = params.getJdbcDriverClassName()
-        project.logger.info("in execSql: url ${url} user ${user} password ${password} driverClassName ${driverClassName}")
-
-        //see http://gradle.1045684.n5.nabble.com/using-jdbc-driver-in-a-task-fails-td1435189.html
-        URLClassLoader loader = GroovyObject.class.classLoader
-
-        project.configurations.driver.each {File file ->
-            loader.addURL(file.toURI().toURL())
-        }
-        Class driverClass = loader.loadClass(driverClassName)
-        project.logger.info("driverClass is ${driverClass}")
-
-        Driver driverInstance = (Driver) driverClass.newInstance()
-        DriverManager.registerDriver(driverInstance)
-
-        Sql db = null
-        try
-        {
-            db = Sql.newInstance(url, user, password)
-            db.execute(sql)
-        }
-        catch (Exception e)
-        {
-            project.logger.error(e.toString())
-        }
-        finally
-        {
-            if (db != null)
-                db.close()
-        }
-    }
-
-    static void dropDatabase(Project project, DatabaseProperties dbProperties)
-    {
-        Properties properties = dbProperties.getConfigProperties()
-        project.logger.info("in dropDatabase for ${project.path}, properties are ${properties}")
-        String toDrop = dbProperties.getJdbcDatabase()
-        if (toDrop == null || toDrop.equals("labkey"))
-        {
-            throw new GradleException("Must specify a database that is not 'labkey'")
-        }
-        else
-        {
-            DatabaseProperties dropProps = new DatabaseProperties(project, dbProperties)
-            // need to connect to the built-in default database in order to drop the database
-            dropProps.setJdbcDatabase(dbProperties.getDefaultDatabase())
-            dropProps.setJdbcUrlParams("")
-
-            project.logger.info("Attempting to drop database ${toDrop}")
-            execSql(project, dropProps, "DROP DATABASE \"${toDrop}\";")
-        }
-    }
-}
\ No newline at end of file

From 2757c4729a11307596a8d1af2430a343660d6b76 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 5 Aug 2025 16:16:34 -0700
Subject: [PATCH 05/61] Add group for `verifyLicensePatch` task

---
 .../groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy b/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy
index 2f91ef0e..d9c4e0d9 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy
@@ -96,8 +96,9 @@ class ApplyLicenses implements Plugin<Project>
             }
 
             project.tasks.register('verifyLicensePatch') {
-                dependsOn(patchApiTask)
-                doLast {
+                it.group = GroupNames.TEST
+                it.dependsOn(patchApiTask)
+                it.doLast {
                     [project.configurations.extJs3Commercial, project.configurations.extJs4Commercial].forEach {
                         def commercialLicense = project.zipTree(it.singleFile).matching {
                             include '*/license.txt'

From 64a77698ffb8deaf6af18e8d146e034fd77214d6 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 8 Aug 2025 07:13:38 -0700
Subject: [PATCH 06/61] Make `getImporterMap` properly visible during
 configuration phase

---
 .../groovy/org/labkey/gradle/task/ClientLibsCompress.groovy    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/ClientLibsCompress.groovy b/src/main/groovy/org/labkey/gradle/task/ClientLibsCompress.groovy
index 782fe1b6..816af2c1 100644
--- a/src/main/groovy/org/labkey/gradle/task/ClientLibsCompress.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/ClientLibsCompress.groovy
@@ -61,7 +61,8 @@ class ClientLibsCompress extends DefaultTask
      * extract the css and javascript files that are referenced.
      * @return map between the file and the importer
      */
-    private Map<File, XmlImporter> getImporterMap()
+    @Internal
+    Map<File, XmlImporter> getImporterMap()
     {
         Map<File, XmlImporter> importerMap = new HashMap<>()
         xmlFiles.files.each() {

From 6ee86cbd412757582478bfed6a74fc69b3e4d61a Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 8 Aug 2025 08:20:58 -0700
Subject: [PATCH 07/61] Use JavaExec task type

---
 .../labkey/gradle/plugin/TestRunner.groovy    | 55 +++++++------------
 1 file changed, 20 insertions(+), 35 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
index 11d80ef5..fd404501 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
@@ -17,6 +17,7 @@ package org.labkey.gradle.plugin
 
 import org.gradle.api.Project
 import org.gradle.api.Task
+import org.gradle.api.tasks.JavaExec
 import org.labkey.gradle.task.RunTestSuite
 import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
@@ -73,45 +74,30 @@ class TestRunner extends UiTest
 
     }
 
-
-    private void addPasswordTasks(Project project)
+    private static void addPasswordTasks(Project project)
     {
-
-        project.tasks.register("setPassword") {
-            Task task ->
+        project.tasks.register("setPassword", JavaExec) {
+            JavaExec task ->
                 task.group = GroupNames.TEST
                 task.description = "Set the password for use in running tests"
-                task.dependsOn(project.tasks.jar)
-                task.doFirst({
-                    project.javaexec({
-                        mainClass = "org.labkey.test.util.PasswordUtil"
-                        classpath {
-                            [project.configurations.uiTestRuntimeClasspath, project.tasks.jar]
-                        }
-                        systemProperties["labkey.server"] = TeamCityPropertiesTask.getLabKeyServer(project)
-                        args = ["set"]
-                        standardInput = System.in
-                    })
-                })
+                task.classpath = project.files(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
+                task.mainClass.set("org.labkey.test.util.PasswordUtil")
+                task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
+                task.args("set")
+                task.standardInput = System.in
         }
 
 
-        project.tasks.register("ensurePassword") {
-            Task task ->
+        project.tasks.register("ensurePassword", JavaExec) {
+            JavaExec task ->
                 task.group = GroupNames.TEST
                 task.description = "Ensure that the password property used for running tests has been set"
                 task.dependsOn(project.tasks.jar)
-                task.doFirst({
-                    project.javaexec({
-                        mainClass = "org.labkey.test.util.PasswordUtil"
-                        classpath {
-                            [project.configurations.uiTestRuntimeClasspath, project.tasks.jar]
-                        }
-                        systemProperties["labkey.server"] = TeamCityPropertiesTask.getLabKeyServer(project)
-                        args = ["ensure"]
-                        standardInput = System.in
-                    })
-                })
+                task.mainClass.set("org.labkey.test.util.PasswordUtil")
+                task.classpath(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
+                task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
+                task.args("ensure")
+                task.standardInput = System.in
         }
     }
 
@@ -127,6 +113,9 @@ class TestRunner extends UiTest
             }
         })
 
+        directories.add(new File("${project.rootDir}/sampledata"))
+        directories.add(new File("${project.rootDir}/${BuildUtils.convertPathToRelativeDir(BuildUtils.getTestProjectPath(project.gradle))}/data"))
+
         File sampleDataFile = BuildUtils.getBuildDirFile(project,"sampledata.dirs")
 
         project.tasks.register("writeSampleDataFile") {
@@ -135,7 +124,7 @@ class TestRunner extends UiTest
                 task.description = "Produce the file with all sampledata directories for use in running tests"
                 task.inputs.files directories
                 task.outputs.file sampleDataFile
-                task..doLast({
+                task.doLast({
                     List<String> dirNames = new ArrayList<>()
 
                     directories.each({File file ->
@@ -147,8 +136,6 @@ class TestRunner extends UiTest
                     try
                     {
                         writer = new OutputStreamWriter(outputStream)
-                        dirNames.add("${project.rootDir}/sampledata")
-                        dirNames.add("${project.rootDir}/${BuildUtils.convertPathToRelativeDir(BuildUtils.getTestProjectPath(project.gradle))}/data")
                         writer.write(String.join(";", dirNames))
                     }
                     finally
@@ -163,8 +150,6 @@ class TestRunner extends UiTest
     private void addTestSuiteTask(Project project)
     {
         project.logger.debug("TestRunner: addTestSuiteTask for ${project.path}")
-        // Using project.tasks.register here cause an error:
-        // Cannot add task 'uiTests' as a task with that name already exists
         project.tasks.register("uiTests", RunTestSuite) {
             RunTestSuite task ->
                 task.group = GroupNames.VERIFICATION

From 3f12de2a010a91efcf8f57adcb9435baed1ab2fa Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 8 Aug 2025 08:26:15 -0700
Subject: [PATCH 08/61] Update release notes

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 5b612b14..63c6a6d4 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,8 @@ on how to do that, including how to develop and test locally and the versioning
 - Update dependency versions
 - Update DoThenSetup and its relatives to be compatible with configuration cache
 - Update DeployApp for better configuration cache compatibility
+- Replace usages of project.javaexc with JavaExc task types
+- Update CompressClientLibs to work better with configuration cache
 
 ### 6.3.0
 *Released*: 3 July 2025

From 717e1ad328d8983964c3573872f5c9a3e96fb725 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 08:28:59 -0700
Subject: [PATCH 09/61] Replace usages of project.javaexec

---
 README.md                                     |  2 +-
 .../org/labkey/gradle/plugin/JsDoc.groovy     | 50 ++++++------
 .../org/labkey/gradle/plugin/TeamCity.groovy  | 76 ++++++++++---------
 .../labkey/gradle/plugin/TestRunner.groovy    |  2 +-
 .../org/labkey/gradle/plugin/XsdDoc.groovy    |  1 +
 .../plugin/extension/JsDocExtension.groovy    |  1 -
 .../labkey/gradle/task/CreateJsDocs.groovy    | 57 +++++++++-----
 .../labkey/gradle/task/CreateXsdDocs.groovy   | 38 +++++-----
 8 files changed, 126 insertions(+), 101 deletions(-)

diff --git a/README.md b/README.md
index 63c6a6d4..7d702aaa 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Update dependency versions
 - Update DoThenSetup and its relatives to be compatible with configuration cache
 - Update DeployApp for better configuration cache compatibility
-- Replace usages of project.javaexc with JavaExc task types
+- Replace usages of project.javaexc with JavaExc task types or injected ExecOperations
 - Update CompressClientLibs to work better with configuration cache
 
 ### 6.3.0
diff --git a/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy b/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
index f6f5b466..58fcdadb 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
@@ -19,8 +19,6 @@ import org.gradle.api.DefaultTask
 import org.gradle.api.Plugin
 import org.gradle.api.Project
 import org.gradle.api.Task
-import org.gradle.api.file.CopySpec
-import org.gradle.api.file.Directory
 import org.gradle.api.tasks.Copy
 import org.gradle.api.tasks.bundling.Zip
 import org.labkey.gradle.plugin.extension.JsDocExtension
@@ -29,6 +27,7 @@ import org.labkey.gradle.util.GroupNames
 import org.labkey.gradle.util.PropertiesUtils
 
 import java.util.regex.Matcher
+
 /**
  * Plugin that provides tasks for created JavaScript documentation using jsDoc tools
  */
@@ -39,43 +38,46 @@ class JsDoc implements Plugin<Project>
     {
         project.extensions.create("jsDoc", JsDocExtension)
         project.jsDoc.root = "${project.rootDir}/tools/jsdoc-toolkit/"
-        project.jsDoc.outputDir = getJsDocDirectory(project).file( "docs").asFile
         addTasks(project)
     }
 
-    static Directory getJsDocDirectory(Project project)
+    public static List<File> getJsFilesToProcess(Project project)
     {
-        return XsdDoc.getClientDocsBuildDir(project).get().dir("javascript")
+        List<File> files = []
+        project.jsDoc.paths.each{ String path ->
+            files += project.file(path)
+        }
+        return files
     }
 
     private static void addTasks(Project project)
     {
         project.tasks.register('jsdocTemplate', Copy) {
-            Copy task ->
-                task.description = "insert the proper version number into the JavaScript documentation"
-                task.configure
-                        { CopySpec copy ->
-                            copy.from project.file("${project.jsDoc.root}/templates/jsdoc")
-                            copy.filter( { String line ->
-                                Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
-                                String newLine = line;
-                                while (matcher.find())
-                                {
-                                    if (matcher.group(1).equals("product.version"))
-                                        newLine = newLine.replace(matcher.group(), (String) project.version)
-                                }
-                                return newLine;
+            Copy copy ->
+                copy.description = "insert the proper version number into the JavaScript documentation"
+                copy.from project.file("${project.jsDoc.root}/templates/jsdoc")
+                copy.inputs.property("version", project.version)
+                copy.filter( { String line ->
+                    Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
+                    String newLine = line;
+                    while (matcher.find())
+                    {
+                        if (matcher.group(1).equals("product.version"))
+                            newLine = newLine.replace(matcher.group(), (String) copy.inputs.properties.get("version"))
+                    }
+                    return newLine;
+
+                })
+                copy.destinationDir = new File((String) "${project.jsDoc.root}/templates/jsdoc_substituted")
 
-                            })
-                            copy.destinationDir = new File((String) "${project.jsDoc.root}/templates/jsdoc_substituted")
-                        }
         }
 
          project.tasks.register("jsdoc", CreateJsDocs) {
              CreateJsDocs task ->
                  task.group = GroupNames.DOCUMENTATION
                  task.description = 'Generating Client API docs'
-                 task.dependsOn(project.tasks.jsdocTemplate)
+                 task.inputs.files project.tasks.jsdocTemplate.outputs.files
+                 task.getFilesToProcess().set(getJsFilesToProcess(project))
          }
 
         project.tasks.register("jsDocZip", Zip) {
@@ -86,7 +88,7 @@ class JsDoc implements Plugin<Project>
                 task.archiveVersion.set(project.getVersion().toString())
                 task.archiveExtension.set("zip")
                 task.from project.tasks.jsdoc
-                task.destinationDirectory.set(getJsDocDirectory(project))
+                task.destinationDirectory.set(CreateJsDocs.getJsDocDirectory(project))
         }
 
         project.tasks.register('cleanJsDoc', DefaultTask) {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 7c5cf72a..bd046eec 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -15,19 +15,29 @@
  */
 package org.labkey.gradle.plugin
 
-import com.sun.jdi.*
+
+import com.sun.jdi.AbsentInformationException
+import com.sun.jdi.Bootstrap
+import com.sun.jdi.IncompatibleThreadStateException
+import com.sun.jdi.ObjectReference
+import com.sun.jdi.StackFrame
+import com.sun.jdi.ThreadReference
+import com.sun.jdi.VMDisconnectedException
+import com.sun.jdi.VirtualMachine
 import com.sun.jdi.connect.AttachingConnector
 import com.sun.jdi.connect.Connector
 import com.sun.jdi.connect.IllegalConnectorArgumentsException
 import org.apache.commons.lang3.SystemUtils
+import org.gradle.api.AntBuilder
 import org.gradle.api.GradleException
 import org.gradle.api.Project
 import org.gradle.api.Task
 import org.gradle.api.UnknownTaskException
+import org.gradle.api.logging.Logger
 import org.gradle.api.provider.Provider
 import org.gradle.api.tasks.Copy
+import org.gradle.api.tasks.JavaExec
 import org.gradle.api.tasks.TaskProvider
-import org.gradle.process.JavaExecSpec
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.PickDb
@@ -83,21 +93,15 @@ class TeamCity extends Tomcat
 
     private void addTasks(Project project)
     {
-        project.tasks.register("setTeamCityAgentPassword") {
-            Task task ->
+        project.tasks.register("setTeamCityAgentPassword", JavaExec) {
+            JavaExec task ->
                 task.group = GroupNames.TEST_SERVER
                 task.description = "Set the password for use in running tests"
                 task.dependsOn(project.tasks.jar)
-                task.doLast {
-                    project.javaexec({ JavaExecSpec spec ->
-                        spec.mainClass = "org.labkey.test.util.PasswordUtil"
-                        spec.classpath {
-                            [project.configurations.uiTestRuntimeClasspath, project.tasks.jar]
-                        }
-                        spec.systemProperties["labkey.server"] = TeamCityPropertiesTask.getLabKeyServer(project)
-                        spec.args = ["set", TeamCityPropertiesTask.getLabKeyUsername(project), TeamCityPropertiesTask.getLabKeyPassword(project)]
-                    })
-                }
+                task.mainClass.set("org.labkey.test.util.PasswordUtil")
+                task.classpath(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
+                task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
+                task.args("set", TeamCityPropertiesTask.getLabKeyUsername(project), TeamCityPropertiesTask.getLabKeyPassword(project))
         }
 
         project.tasks.register("cleanTestLogs") {
@@ -111,8 +115,8 @@ class TeamCity extends Tomcat
         }
 
         project.tasks.named("stopTomcat").configure {
-            doLast {
-                ensureShutdown(project)
+            it.doLast {
+                ensureShutdown(it.logger)
             }
         }
 
@@ -121,7 +125,7 @@ class TeamCity extends Tomcat
                 task.group = GroupNames.TEST_SERVER
                 task.description = "Kill Chrome processes"
                 task.doLast {
-                    killChrome(project)
+                    killChrome(it.ant)
                 }
         }
 
@@ -130,7 +134,7 @@ class TeamCity extends Tomcat
                 task.group = GroupNames.TEST_SERVER
                 task.description = "Kill Firefox processes"
                 task.doLast {
-                    killFirefox(project)
+                    killFirefox(it.ant)
                 }
         }
 
@@ -154,13 +158,14 @@ class TeamCity extends Tomcat
                 task.description = "Create NLP engine configs for the test server"
                 task.from BuildUtils.getServerProject(project).file(TEST_CONFIGS_DIR)
                 task.include NLP_CONFIG_FILE
+                task.inputs.property("directoryPath", new File((String) project.labkey.externalDir, "nlp/nlp_engine.py").getAbsolutePath())
                 task.filter({ String line ->
                     Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
                     String newLine = line
                     while (matcher.find())
                     {
                         if (matcher.group(1).equals("enginePath"))
-                            newLine = newLine.replace(matcher.group(), new File((String) project.labkey.externalDir, "nlp/nlp_engine.py").getAbsolutePath())
+                            newLine = newLine.replace(matcher.group(), (String) task.inputs.properties.get("directoryPath"))
                     }
                     return newLine
                 }
@@ -296,7 +301,7 @@ class TeamCity extends Tomcat
                 task.description = "Run a test suite on the TeamCity server"
                 task.doLast(
              {
-                        killFirefox(project)
+                        killFirefox(task.ant)
                     }
                 )
         }
@@ -305,60 +310,60 @@ class TeamCity extends Tomcat
         }
     }
 
-    private static void killChrome(Project project)
+    private static void killChrome(AntBuilder ant)
     {
         if (SystemUtils.IS_OS_WINDOWS)
         {
-            project.ant.exec(executable: "taskkill")
+            ant.exec(executable: "taskkill")
                     {
                         arg(line:"/F /IM chromedriver.exe" )
                     }
-            project.ant.exec(executable: "taskkill")
+            ant.exec(executable: "taskkill")
                     {
                         arg(line:"/F /IM chrome.exe" )
                     }
         }
         else if (SystemUtils.IS_OS_UNIX)
         {
-            project.ant.exec(executable: "killall")
+            ant.exec(executable: "killall")
                     {
                         arg(line:  "-q -KILL chromedriver")
                     }
-            project.ant.exec(executable: "killall")
+            ant.exec(executable: "killall")
                     {
                         arg(line: "-q -KILL chrome")
                     }
-            project.ant.exec(executable: "killall")
+            ant.exec(executable: "killall")
                     {
                         arg(line: "-q KILL BrowserBlocking")
                     }
         }
     }
 
-    private static void killFirefox(Project project)
+    private static void killFirefox(AntBuilder ant)
     {
         if (SystemUtils.IS_OS_WINDOWS)
         {
-            project.ant.exec(executable: "taskkill")
+            ant.exec(executable: "taskkill")
                     {
                         arg(line: "/F /IM firefox.exe")
                     }
-            project.ant.exec(executable: "taskkill")
+            ant.exec(executable: "taskkill")
                     {
                         arg(line: "/F /IM geckodriver.exe")
                     }
         }
         else if (SystemUtils.IS_OS_UNIX)
         {
-            project.ant.exec(executable: "killall")
+            ant.exec(executable: "killall")
                     {
                         arg(line: "-q firefox")
                     }
-            project.ant.exec(executable: "killall")
+            ant.exec(executable: "killall")
                     {
                         arg(line: "-q firefox-bin")
                     }
-            project.ant.exec(executable: "killall")
+            ant.exec(executable: "killall")
                     {
                         arg(line: "-q geckodriver")
                     }
@@ -406,7 +411,6 @@ class TeamCity extends Tomcat
         catch (VMDisconnectedException ignore)
         {
             println("VM at localhost:" + port + " exited normally")
-            return
         }
     }
 
@@ -475,18 +479,18 @@ class TeamCity extends Tomcat
         }
     }
 
-    private void ensureShutdown(Project project)
+    private void ensureShutdown(Logger logger)
     {
         String debugPort = extension.getTeamCityProperty("tomcat.debug")
         if (!debugPort.isEmpty())
         {
-            project.logger.debug("Ensuring shutdown using port ${debugPort}")
+            logger.debug("Ensuring shutdown using port ${debugPort}")
             try
             {
                 AttachingConnector socketConnector = null
                 for (AttachingConnector connector : Bootstrap.virtualMachineManager().attachingConnectors())
                 {
-                    project.logger.debug("Found connector ${connector.name()} with class ${connector.getClass().getName()}")
+                    logger.debug("Found connector ${connector.name()} with class ${connector.getClass().getName()}")
                     if ("com.sun.jdi.SocketAttach".equals(connector.name()))
                     {
                         socketConnector = connector
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
index fd404501..14dcdf58 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
@@ -80,7 +80,7 @@ class TestRunner extends UiTest
             JavaExec task ->
                 task.group = GroupNames.TEST
                 task.description = "Set the password for use in running tests"
-                task.classpath = project.files(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
+                task.classpath(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
                 task.mainClass.set("org.labkey.test.util.PasswordUtil")
                 task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
                 task.args("set")
diff --git a/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy b/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy
index 95ebca4d..7b71c851 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy
@@ -59,6 +59,7 @@ class XsdDoc implements Plugin<Project>
            CreateXsdDocs task ->
                task.group = GroupNames.DOCUMENTATION
                task.description = 'Generating documentation for classes generated from XSD files'
+               task.getFilesToProcess().set(Arrays.asList(project.xsdDoc.xsdFiles))
        }
 
         project.tasks.register("xsdDocZip", Zip) {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/JsDocExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/JsDocExtension.groovy
index 4f15f663..d847da62 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/JsDocExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/JsDocExtension.groovy
@@ -19,5 +19,4 @@ class JsDocExtension
 {
     String root
     String[] paths = []
-    File outputDir
 }
diff --git a/src/main/groovy/org/labkey/gradle/task/CreateJsDocs.groovy b/src/main/groovy/org/labkey/gradle/task/CreateJsDocs.groovy
index 211bf06c..a84c52a7 100644
--- a/src/main/groovy/org/labkey/gradle/task/CreateJsDocs.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/CreateJsDocs.groovy
@@ -16,40 +16,57 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
-import org.gradle.api.tasks.InputFiles
+import org.gradle.api.Project
+import org.gradle.api.file.Directory
+import org.gradle.api.file.DirectoryProperty
+import org.gradle.api.provider.ListProperty
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.InputDirectory
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
+import org.gradle.process.ExecOperations
+import org.labkey.gradle.plugin.XsdDoc
 
-class CreateJsDocs extends DefaultTask
+import javax.inject.Inject
+
+abstract class CreateJsDocs extends DefaultTask
 {
-    @InputFiles
-    List<File> getInputFiles()
-    {
-        List<File> files = []
-        project.jsDoc.paths.each{ String path ->
-            files += project.file(path)
-        }
-        return files
-    }
+    @Inject abstract ExecOperations getExec()
+
+    @InputDirectory
+    final abstract DirectoryProperty templateDir = project.objects.directoryProperty().convention(
+            project.rootProject.layout.projectDirectory.dir("tools/jsdoc-toolkit/templates/jsdoc_substituted")
+    )
+
+    @Input
+    final abstract Property<String> jarPath = project.objects.property(String).convention("${project.jsDoc.root}/jsrun.jar")
+
+    @Input
+    final abstract Property<String> jsPath = project.objects.property(String).convention("${project.jsDoc.root}/app/run.js")
 
     @OutputDirectory
-    File getOutputDirectory()
+    final abstract DirectoryProperty outputDir = project.objects.directoryProperty().convention(getJsDocDirectory(project).dir( "docs"))
+
+    @Input
+    abstract ListProperty<File> getFilesToProcess()
+
+    static Directory getJsDocDirectory(Project project)
     {
-        return project.jsDoc.outputDir
+        return XsdDoc.getClientDocsBuildDir(project).get().dir("javascript")
     }
 
     @TaskAction
     void createDocs()
     {
-        List<File> inputPaths = getInputFiles()
-        project.javaexec { exec ->
+        exec.javaexec { exec ->
             exec.mainClass = "-jar"
-            exec.args = ["${project.jsDoc.root}/jsrun.jar",
-                         "${project.jsDoc.root}/app/run.js",
-                         "--template=${project.tasks.jsdocTemplate.destinationDir}",
-                         "--directory=${getOutputDirectory()}",
+            exec.args = [jarPath.get(),
+                         jsPath.get(),
+                         "--template=${templateDir.get()}",
+                         "--directory=${outputDir.get()}",
                          "--verbose"]
-            inputPaths.each { File file ->
+            filesToProcess.get().each { File file ->
                 exec.args += file.path
             }
         }
diff --git a/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy b/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy
index eb7b84d0..8995c6a1 100644
--- a/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy
@@ -16,30 +16,31 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.file.DirectoryProperty
+import org.gradle.api.provider.ListProperty
+import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
+import org.gradle.process.ExecOperations
 import org.labkey.gradle.plugin.XsdDoc
 
-class CreateXsdDocs extends DefaultTask
+import javax.inject.Inject
+
+abstract class CreateXsdDocs extends DefaultTask
 {
-    @InputFiles
-    List<File> getXsdFiles()
-    {
-        return project.xsdDoc.xsdFiles
-    }
+    @Inject abstract ExecOperations getExec()
+
+    @Input
+    abstract ListProperty<File> getFilesToProcess()
 
     @OutputDirectory
-    File getOutputDirectory()
-    {
-        return XsdDoc.getXsdDocDirectory(project).file( "docs").asFile
-    }
+    final abstract DirectoryProperty outputDir = project.objects.directoryProperty().convention(XsdDoc.getXsdDocDirectory(project).dir( "docs"))
 
     @TaskAction
     void createDocs()
     {
-        List<File> xsdFiles = getXsdFiles()
-        project.javaexec {exec ->
+        exec.javaexec {exec ->
             exec.mainClass = "com.docflex.xml.Generator"
 
             exec.classpath project.configurations.xsdDoc
@@ -48,15 +49,16 @@ class CreateXsdDocs extends DefaultTask
                     "-template", "${project.rootDir}/tools/docflex-xml-re-${project.docflexXmlReVersion}/templates/XSDDoc/FramedDoc.tpl",
                     "-p:docTitle", "LabKey XML Schema Reference",
                     "-format", "HTML", // output format
-                    "-d", getOutputDirectory(), // output directory
+                    "-d", outputDir.get().asFile.getAbsolutePath(), // output directory
                     "-nodialog", // do not launch the generator GUI
                     "-launchviewer=false", //  do not launch the default viewer for the output file
             ]
-            //     Specify one or many data source XML files to be processed
-            //     by the specified template. (Both local pathnames and URLs
-            //     are allowed.)
-            xsdFiles.each {File file ->
-                exec.args += file.path
+            // Specify one or many data source XML files to be processed
+            // by the specified template. (Both local pathnames and URLs
+            // are allowed.)
+            filesToProcess.get().each {
+                File file ->
+                    exec.args += file.path
             }
         }
     }

From cfbd2236d8fe33c92924742c726de2ba2dba4c46 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 08:56:42 -0700
Subject: [PATCH 10/61] Use DeleteTask instead of DefaultTask

---
 .../groovy/org/labkey/gradle/plugin/JsDoc.groovy   | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy b/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
index 58fcdadb..5f4fdaf0 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
@@ -19,7 +19,9 @@ import org.gradle.api.DefaultTask
 import org.gradle.api.Plugin
 import org.gradle.api.Project
 import org.gradle.api.Task
+import org.gradle.api.file.DeleteSpec
 import org.gradle.api.tasks.Copy
+import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.bundling.Zip
 import org.labkey.gradle.plugin.extension.JsDocExtension
 import org.labkey.gradle.task.CreateJsDocs
@@ -91,14 +93,14 @@ class JsDoc implements Plugin<Project>
                 task.destinationDirectory.set(CreateJsDocs.getJsDocDirectory(project))
         }
 
-        project.tasks.register('cleanJsDoc', DefaultTask) {
-            Task task ->
+        project.tasks.register('cleanJsDoc', Delete) {
+            Delete task ->
                 task.group = GroupNames.DOCUMENTATION
                 task.description = "Remove files created by jsdoc and jsDocZip tasks"
-                task.doFirst( {
-                    project.delete(project.tasks.jsDocZip.outputs)
-                    project.delete(project.tasks.jsdoc.outputs)
-                })
+                task.configure { DeleteSpec delete ->
+                    delete.delete(project.tasks.jsDocZip.outputs)
+                    delete.delete(project.tasks.jsdoc.outputs)
+                }
         }
     }
 }

From 3a8595171d6d530e96c104e102050a06f749ebc3 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 09:05:20 -0700
Subject: [PATCH 11/61] Use DeleteTask instead of DefaultTask

---
 .../org/labkey/gradle/plugin/XsdDoc.groovy       | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy b/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy
index 7b71c851..ef8278b0 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/XsdDoc.groovy
@@ -15,12 +15,13 @@
  */
 package org.labkey.gradle.plugin
 
-import org.gradle.api.DefaultTask
+
 import org.gradle.api.Plugin
 import org.gradle.api.Project
-import org.gradle.api.Task
+import org.gradle.api.file.DeleteSpec
 import org.gradle.api.file.Directory
 import org.gradle.api.provider.Provider
+import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.bundling.Zip
 import org.labkey.gradle.plugin.extension.XsdDocExtension
 import org.labkey.gradle.task.CreateXsdDocs
@@ -59,6 +60,7 @@ class XsdDoc implements Plugin<Project>
            CreateXsdDocs task ->
                task.group = GroupNames.DOCUMENTATION
                task.description = 'Generating documentation for classes generated from XSD files'
+               task.xsdDocClasspath.setFrom(project.configurations.xsdDoc)
                task.getFilesToProcess().set(Arrays.asList(project.xsdDoc.xsdFiles))
        }
 
@@ -74,13 +76,13 @@ class XsdDoc implements Plugin<Project>
                 task.dependsOn(project.tasks.xsddoc)
         }
 
-        project.tasks.register("cleanXsdDoc", DefaultTask) {
-            Task task ->
+        project.tasks.register("cleanXsdDoc", Delete) {
+            Delete task ->
                 task.group = GroupNames.DOCUMENTATION
                 task.description = "Remove files created by xsddoc and xsdDocZip tasks"
-                task.doFirst({
-                    project.delete(project.tasks.xsdDocZip.outputs)
-                    project.delete(project.tasks.xsddoc.outputs)
+                task.configure({ DeleteSpec delete ->
+                    delete.delete(project.tasks.xsdDocZip.outputs)
+                    delete.delete(project.tasks.xsddoc.outputs)
                 })
         }
     }

From 8892e0244a6beb93ca4e6817eddf6962e9917bb0 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 09:05:45 -0700
Subject: [PATCH 12/61] Set up properties for project-related values

---
 .../org/labkey/gradle/task/CreateXsdDocs.groovy  | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy b/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy
index 8995c6a1..6777d7c5 100644
--- a/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/CreateXsdDocs.groovy
@@ -16,8 +16,11 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.file.ConfigurableFileCollection
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.provider.ListProperty
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Classpath
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.OutputDirectory
@@ -37,19 +40,26 @@ abstract class CreateXsdDocs extends DefaultTask
     @OutputDirectory
     final abstract DirectoryProperty outputDir = project.objects.directoryProperty().convention(XsdDoc.getXsdDocDirectory(project).dir( "docs"))
 
+    @Input
+    final abstract Property<String> templatePath = project.objects.property(String).convention("${project.rootDir}/tools/docflex-xml-re-${project.docflexXmlReVersion}/templates/XSDDoc/FramedDoc.tpl")
+
+    @InputFiles
+    @Classpath
+    abstract ConfigurableFileCollection getXsdDocClasspath()
+
     @TaskAction
     void createDocs()
     {
         exec.javaexec {exec ->
             exec.mainClass = "com.docflex.xml.Generator"
 
-            exec.classpath project.configurations.xsdDoc
+            exec.classpath getXsdDocClasspath()
 
             exec.args = [
-                    "-template", "${project.rootDir}/tools/docflex-xml-re-${project.docflexXmlReVersion}/templates/XSDDoc/FramedDoc.tpl",
+                    "-template", templatePath.get(),
                     "-p:docTitle", "LabKey XML Schema Reference",
                     "-format", "HTML", // output format
-                    "-d", outputDir.get().asFile.getAbsolutePath(), // output directory
+                    "-d", outputDir.get().asFile.getAbsolutePath(),
                     "-nodialog", // do not launch the generator GUI
                     "-launchviewer=false", //  do not launch the default viewer for the output file
             ]

From 9292a330d78453b2fbcc2d5f6de9bc52b8d04122 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 09:32:50 -0700
Subject: [PATCH 13/61] Use `Delete` task instead of `DefaultTask`

---
 .../org/labkey/gradle/plugin/ServerDeploy.groovy     | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index e309235c..07164a07 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -208,12 +208,12 @@ class ServerDeploy implements Plugin<Project>
         if (BuildUtils.embeddedProjectExists(project)) {
             def embeddedProject = project.project(BuildUtils.getEmbeddedProjectPath())
 
-            project.tasks.register("cleanEmbeddedDeploy", DefaultTask) {
-                DefaultTask task ->
+            project.tasks.register("cleanEmbeddedDeploy", Delete) {
+                Delete task ->
                     task.group = GroupNames.DEPLOY
                     task.description = "Remove the ${embeddedDir} directory"
-                    task.doLast {
-                        project.delete embeddedDir
+                    task.configure { DeleteSpec delete ->
+                        delete.delete embeddedDir
                     }
             }
             project.tasks.named('deployApp').configure {
@@ -253,14 +253,14 @@ class ServerDeploy implements Plugin<Project>
         // This may prevent multiple Tomcat restarts
         project.tasks.named('setup').configure {mustRunAfter(project.tasks.stageDistribution)}
 
-        project.tasks.register('undeployModules',UndeployModules) {
+        project.tasks.register('undeployModules', UndeployModules) {
             UndeployModules task ->
                 task.group = GroupNames.DEPLOY
                 task.description = "Removes all module files and directories from the deploy and staging directories"
         }
 
         project.tasks.register(
-                'cleanStaging',Delete) {
+                'cleanStaging', Delete) {
             Delete task ->
                 task.group = GroupNames.DEPLOY
                 task.description = "Removes the staging directory ${stagingDir}"

From 8fa23bb9a4b2e43d2f0ea39a774af1b971d0b511 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 09:33:13 -0700
Subject: [PATCH 14/61] Make `useSsl` an input property for configuration cache
 compatibility

---
 src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy b/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
index 1263c6c0..86ef8b0a 100644
--- a/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
@@ -16,6 +16,8 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.util.PropertiesUtils
@@ -29,12 +31,15 @@ class StopLabKey extends DefaultTask
     @InputFile
     File propertiesFile = BuildUtils.getApplicationPropertiesFile(project)
 
+    @Input
+    final abstract Property<Boolean> useSsl = project.objects.property(Boolean).convention(project.hasProperty("useSsl"))
+
     @TaskAction
     void action()
     {
         def applicationProperties = PropertiesUtils.getApplicationProperties(propertiesFile)
         def port = applicationProperties.getProperty("management.server.port", applicationProperties.getProperty("server.port"))
-        def endpoint =  "${project.hasProperty("useSsl") ? "https" : "http"}://localhost:$port/actuator/shutdown"
+        def endpoint =  "${useSsl.get() ? "https" : "http"}://localhost:$port/actuator/shutdown"
         def command = "curl -X POST $endpoint"
         this.logger.info("Sending command to $endpoint")
         def proc = command.execute()

From 942c7956f067dc5c3ed7aa7a065dd543d432d80a Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 09:33:35 -0700
Subject: [PATCH 15/61] Remove `listNodeProjects` task

---
 .../org/labkey/gradle/plugin/NpmRun.groovy    | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/NpmRun.groovy b/src/main/groovy/org/labkey/gradle/plugin/NpmRun.groovy
index 70d12891..b18821c2 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/NpmRun.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/NpmRun.groovy
@@ -170,24 +170,7 @@ class NpmRun implements Plugin<Project>
             }
         }
 
-        project.tasks.register("listNodeProjects") {
-            Task task ->
-                task.group = GroupNames.NPM_RUN
-                task.description = "List all projects that employ node in their build"
-                task.doLast({
-                    List<String> nodeProjects = []
-                    project.allprojects({Project p ->
-                        if (p.getPlugins().hasPlugin(NpmRun.class))
-                            nodeProjects.add(p.path)
-                    })
-                    if (nodeProjects.size() == 0)
-                        println("No projects found containing ${NPM_PROJECT_FILE}")
-                    else {
-                        println("The following projects use Node in their builds:\n\t${nodeProjects.join("\n\t")}\n")
-                    }
-                })
-                task.notCompatibleWithConfigurationCache("Needs to walk the project tree")
-        }
+
 
     }
 

From 54e90eb4fee83545dc95c9672a2e5e2344459842 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 09:33:49 -0700
Subject: [PATCH 16/61] Update release notes

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7d702aaa..656822fd 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,8 @@ on how to do that, including how to develop and test locally and the versioning
 - Update DoThenSetup and its relatives to be compatible with configuration cache
 - Update DeployApp for better configuration cache compatibility
 - Replace usages of project.javaexc with JavaExc task types or injected ExecOperations
-- Update CompressClientLibs to work better with configuration cache
+- Update CompressClientLibs, StopLabKey to work better with configuration cache
+- Remove `listNodeModules` task defined by `NpmRun` plugin
 
 ### 6.3.0
 *Released*: 3 July 2025

From 9af31f2a9d73c60ff6967fe2aa354d29dec2e19f Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:29:48 -0700
Subject: [PATCH 17/61] Remove `listJsp` task

---
 src/main/groovy/org/labkey/gradle/plugin/Jsp.groovy | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/Jsp.groovy b/src/main/groovy/org/labkey/gradle/plugin/Jsp.groovy
index a2ebb656..be8c1535 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Jsp.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Jsp.groovy
@@ -109,17 +109,6 @@ class Jsp implements Plugin<Project>
 
     private static void addJspTasks(Project project)
     {
-        project.tasks.register('listJsps') {
-            Task task ->
-                task.group = GroupNames.JSP
-                task.doLast {
-                    getJspFileTree(project).each ({
-                        println it.absolutePath
-                    })
-                }
-        }
-
-
         project.tasks.register('copyJsp', CopyJsp) {
             CopyJsp task ->
                 task.group = GroupNames.JSP

From 8b5b7e18e51652174d4e0dccca6d07c8afc1ceb2 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:30:35 -0700
Subject: [PATCH 18/61] Remove `cleanOut` task

---
 .../labkey/gradle/plugin/FileModule.groovy    | 23 ++++++++-----------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
index 61584ba8..c2b3d710 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
@@ -137,19 +137,6 @@ class FileModule implements Plugin<Project>
                 task.outputs.cacheIf { false } // disable build caching. Has too many undeclared inputs.
         }
 
-        // This is added because Intellij started creating this "out" directory when you build through IntelliJ.
-        // It copies files there that are actually input files to the build, which causes some problems when later
-        // builds attempt to find their input files.
-        project.tasks.register("cleanOut", Delete) {
-            Delete task ->
-                task.group = GroupNames.BUILD
-                task.description = "removes the ${project.file('out')} directory created by Intellij builds"
-                task.configure({ Delete delete ->
-                    if (project.file("out").isDirectory())
-                        project.delete project.file("out")
-                })
-        }
-
         var moduleTask = project.tasks.register("module", Jar) {
             Jar jar ->
                 jar.group = GroupNames.MODULE
@@ -209,6 +196,12 @@ class FileModule implements Plugin<Project>
                 }
             }
 
+        project.tasks.named('deployModule')
+            {
+                notCompatibleWithConfigurationCache("Needs its own class to do the two copies (one to staging and one to deploy.")
+            }
+
+
         project.tasks.register('undeployModule', Delete) {
             Delete task ->
                 task.group = GroupNames.MODULE
@@ -232,6 +225,10 @@ class FileModule implements Plugin<Project>
                 }
         }
 
+        project.tasks.named('undeployModule')
+                {
+                    notCompatibleWithConfigurationCache("Need a good way to pick up all the module files and directories. Will likely required its own class with various task outputs as inputs.")
+                }
 
         project.tasks.register("reallyClean") {
             Task task ->

From a8478542ea22b1527fe82fce9a3d5c870010f3e8 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:31:16 -0700
Subject: [PATCH 19/61] Remove unused code for artifact publication (seems
 unlikely that we will do this)

---
 .../labkey/gradle/plugin/Distribution.groovy  | 72 -------------------
 1 file changed, 72 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy b/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
index a00baec4..ea4015fa 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
@@ -63,10 +63,6 @@ class Distribution implements Plugin<Project>
         addDependencies(project)
         addTasks(project)
         addTaskDependencies(project)
-
-        // commented out until we start publishing distribution artifacts, and then we'll examine the publications more closely
-//        if (BuildUtils.shouldPublishDistribution(project))
-//            addArtifacts(project)
     }
 
     private void addConfigurations(Project project)
@@ -170,74 +166,6 @@ class Distribution implements Plugin<Project>
                     project.dependencies.add("distribution", dep)
         }
     }
-
-    private void addArtifacts(Project project)
-    {
-        project.apply plugin: 'maven-publish'
-
-        // TODO this is really only an approximation of what's needed. We don't currently publish distribution artifacts
-        // to artifactory
-        project.afterEvaluate {
-            String artifactId = getArtifactId(project)
-            Properties pomProperties = LabKeyExtension.getApiPomProperties(artifactId, project.dist.description, project)
-            project.publishing {
-                publications {
-                    distributions(MavenPublication) { pub ->
-                        pub.artifactId(artifactId)
-                        project.tasks.each {
-                            if (it instanceof ModuleDistribution)
-                            {
-                                it.outputs.files.each {File file ->
-                                    pub.artifact(file)
-                                    {
-                                        String fileName = file.getName()
-                                        if (fileName.endsWith("gz"))
-                                            extension "tar.gz"
-                                        if (fileName.contains("-src."))
-                                            classifier "src"
-                                    }
-                                }
-                            }
-                        }
-                        pom {
-                            name = project.name
-                            description = pomProperties.getProperty("Description")
-                            url = PomFileHelper.LABKEY_ORG_URL
-                            developers PomFileHelper.getLabKeyTeamDevelopers()
-                            // TODO this should probably not always be Apache license
-//                            licenses pomUtil.getLicense()
-                            organization PomFileHelper.getLabKeyOrganization()
-//                            scm PomFileHelper.getLabKeyScm()
-                            // doesn't seem like these pom files will have any dependencies
-                        }
-                    }
-                }
-
-                project.artifactoryPublish {
-                    project.tasks.each {
-                        if (it instanceof ModuleDistribution)
-                        {
-                            dependsOn it
-                        }
-                    }
-                    publications('distributions')
-                }
-            }
-        }
-    }
-
-    static String getArtifactId(Project project)
-    {
-        if (project.dist.artifactId != null)
-            return project.dist.artifactId
-        else
-        {
-            return TaskUtils.getOptionalTask(project, "distribution")
-                    .filter(task -> task.get() instanceof ModuleDistribution)
-                    .map(task -> ((ModuleDistribution)task.get()).getArtifactId())
-                    .orElse(project.name)
-        }
-    }
 }
 
 

From 096b44f6c647275e695f84dafbed9c8179202a09 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:31:23 -0700
Subject: [PATCH 20/61] Release notes

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 656822fd..77ff9503 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Replace usages of project.javaexc with JavaExc task types or injected ExecOperations
 - Update CompressClientLibs, StopLabKey to work better with configuration cache
 - Remove `listNodeModules` task defined by `NpmRun` plugin
+- Remove `cleanOut` task defined by `FileModule` plugin
 
 ### 6.3.0
 *Released*: 3 July 2025

From f78dabf22ea9232dd61c79b3830b0156a2d5ae1b Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:43:52 -0700
Subject: [PATCH 21/61] update comment on compatibility

---
 src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
index c2b3d710..52b5fcd7 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
@@ -198,7 +198,7 @@ class FileModule implements Plugin<Project>
 
         project.tasks.named('deployModule')
             {
-                notCompatibleWithConfigurationCache("Needs its own class to do the two copies (one to staging and one to deploy.")
+                notCompatibleWithConfigurationCache("Needs its own class to do the two copies (one to staging and one to deploy or possibly two Copy tasks chained together.")
             }
 
 

From 59edebca0d71891a5a117c5efa29da3bc29237df Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:45:50 -0700
Subject: [PATCH 22/61] Remove `cleanAndDeploy` task

---
 README.md                                                | 1 +
 .../groovy/org/labkey/gradle/plugin/ServerDeploy.groovy  | 9 ---------
 2 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 77ff9503..54a85482 100644
--- a/README.md
+++ b/README.md
@@ -24,6 +24,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Update CompressClientLibs, StopLabKey to work better with configuration cache
 - Remove `listNodeModules` task defined by `NpmRun` plugin
 - Remove `cleanOut` task defined by `FileModule` plugin
+- Revemo `cleanAndDeploy` task from `ServerDeploy` plugin
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index 07164a07..c7e07806 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -281,15 +281,6 @@ class ServerDeploy implements Plugin<Project>
         }
         project.tasks.named('deployApp').configure {mustRunAfter(project.tasks.cleanDeploy)}
 
-        project.tasks.register("cleanAndDeploy", DeployApp) {
-            DeployApp task ->
-                task.group = GroupNames.DEPLOY
-                task.binaries.setFrom(project.configurations.binaries)
-                task.description = "Removes the deploy directory ${deployDir} then deploys the application locally"
-                task.dependsOn(project.tasks.cleanDeploy)
-                task.notCompatibleWithConfigurationCache("TODO 'cannot serialize project' error, but unclear where it comes from")
-        }
-
         project.tasks.register("cleanBuild", Delete) {
             Delete task ->
                 task.group = GroupNames.DEPLOY

From f7d4bada3123bb92c874163bd9a7a526c38c4659 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:57:32 -0700
Subject: [PATCH 23/61] Use Delete task instead of Default task for config
 cache compatibility

---
 .../groovy/org/labkey/gradle/plugin/TeamCity.groovy    | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index bd046eec..ea1ccc14 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -33,9 +33,11 @@ import org.gradle.api.GradleException
 import org.gradle.api.Project
 import org.gradle.api.Task
 import org.gradle.api.UnknownTaskException
+import org.gradle.api.file.DeleteSpec
 import org.gradle.api.logging.Logger
 import org.gradle.api.provider.Provider
 import org.gradle.api.tasks.Copy
+import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.JavaExec
 import org.gradle.api.tasks.TaskProvider
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
@@ -104,13 +106,13 @@ class TeamCity extends Tomcat
                 task.args("set", TeamCityPropertiesTask.getLabKeyUsername(project), TeamCityPropertiesTask.getLabKeyPassword(project))
         }
 
-        project.tasks.register("cleanTestLogs") {
-            Task task ->
+        project.tasks.register("cleanTestLogs", Delete) {
+            Delete task ->
                 task.group = GroupNames.TEST_SERVER
                 task.description = "Removes log files from Tomcat and TeamCity"
                 task.dependsOn project.tasks.cleanLogs
-                task.doLast {
-                    project.delete "${project.projectDir}/${TEAMCITY_INFO_FILE}"
+                task.configure { DeleteSpec delete ->
+                    delete.delete "${project.projectDir}/${TEAMCITY_INFO_FILE}"
                 }
         }
 

From ab7fc8bebb334caf7d5ffd5b3a6a0495b73b44de Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 10:58:50 -0700
Subject: [PATCH 24/61] Update `CopyAndInstallRPackage` Task class to use
 injected FileSystem instead of `project.copy`

---
 README.md                                                | 3 ++-
 .../org/labkey/gradle/task/CopyAndInstallRPackage.groovy | 9 +++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 54a85482..d4b549e0 100644
--- a/README.md
+++ b/README.md
@@ -24,7 +24,8 @@ on how to do that, including how to develop and test locally and the versioning
 - Update CompressClientLibs, StopLabKey to work better with configuration cache
 - Remove `listNodeModules` task defined by `NpmRun` plugin
 - Remove `cleanOut` task defined by `FileModule` plugin
-- Revemo `cleanAndDeploy` task from `ServerDeploy` plugin
+- Remove `cleanAndDeploy` task from `ServerDeploy` plugin
+- Update `CopyAndInstallRPackage` Task class to use injected FileSystem instead of `project.copy`
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/task/CopyAndInstallRPackage.groovy b/src/main/groovy/org/labkey/gradle/task/CopyAndInstallRPackage.groovy
index 8b888a56..f231447d 100644
--- a/src/main/groovy/org/labkey/gradle/task/CopyAndInstallRPackage.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/CopyAndInstallRPackage.groovy
@@ -2,12 +2,17 @@ package org.labkey.gradle.task
 
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DuplicatesStrategy
+import org.gradle.api.file.FileSystemOperations
 import org.gradle.api.tasks.InputDirectory
 import org.gradle.api.tasks.TaskAction
 import org.gradle.api.tasks.TaskExecutionException
 
-class CopyAndInstallRPackage extends InstallRPackage
+import javax.inject.Inject
+
+abstract class CopyAndInstallRPackage extends InstallRPackage
 {
+    @Inject abstract FileSystemOperations getFs()
+
     @InputDirectory
     File packageLocation
 
@@ -22,7 +27,7 @@ class CopyAndInstallRPackage extends InstallRPackage
 
         super.doInstall() // Install dependencies
         File rLibsUserDir = getInstallDir()
-        project.copy {
+        fs.copy {
             CopySpec copy ->
                 copy.from packageLocation
                 copy.into(rLibsUserDir)

From 67764b413a946d7745b5c6ba50fb9b45291fd7f3 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 11:05:50 -0700
Subject: [PATCH 25/61] Use Task ant, not project.ant

---
 .../groovy/org/labkey/gradle/task/CreateModule.groovy  | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/CreateModule.groovy b/src/main/groovy/org/labkey/gradle/task/CreateModule.groovy
index 18af823e..8ca8fe23 100644
--- a/src/main/groovy/org/labkey/gradle/task/CreateModule.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/CreateModule.groovy
@@ -47,7 +47,7 @@ class CreateModule extends DefaultTask
             moduleName =  project.moduleName
         }
         else {
-            project.ant.input(
+            ant.input(
                     message: "\nEnter the (Java) name for your new module: ",
                     addProperty: "new_moduleName"
             )
@@ -65,7 +65,7 @@ class CreateModule extends DefaultTask
             moduleDestination =  project.moduleDestination
         }
         else {
-            project.ant.input(
+            ant.input(
                     message: "\nEnter the location for the new module (absolute or relative to '" + project.projectDir.getAbsolutePath() + "'): ",
                     addProperty: "new_moduleDestination"
             )
@@ -93,19 +93,19 @@ class CreateModule extends DefaultTask
             createApiFiles = ((String)project.createFiles).contains('api')
         }
         else {
-            project.ant.input(
+            ant.input(
                     message: "\nWill this module create and manage a database schema? (Y/n)",
                     addProperty: "new_hasManagedSchema"
             )
             hasManagedSchema = !(ant.new_hasManagedSchema.trim().equalsIgnoreCase("n"))
 
-            project.ant.input(
+            ant.input(
                     message: "\nCreate test stubs (y/N)",
                     addProperty: "new_createTestFiles"
             )
             createTestFiles = ant.new_createTestFiles.trim().equalsIgnoreCase("y")
 
-            project.ant.input(
+            ant.input(
                     message: "\nCreate API stubs (y/N)",
                     addProperty: "new_createApiFiles"
             )

From fec17e4b918ffc36c78deed39825a02896b116ac Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 11:09:31 -0700
Subject: [PATCH 26/61] Use task logger and ant

---
 src/main/groovy/org/labkey/gradle/task/GzipAction.groovy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/GzipAction.groovy b/src/main/groovy/org/labkey/gradle/task/GzipAction.groovy
index e6d0148c..36a6cf97 100644
--- a/src/main/groovy/org/labkey/gradle/task/GzipAction.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/GzipAction.groovy
@@ -40,11 +40,11 @@ class GzipAction implements Action<Task>
         }
 
         tree.each { File file ->
-            task.project.ant.gzip(
+            task.ant.gzip(
                     src: file,
                     destfile: "${file.toString()}.gz"
             )
-            task.project.logger.info("zipping file " + file + " to ${file.toString()}.gz")
+            task.logger.info("zipping file " + file + " to ${file.toString()}.gz")
         }
     }
 }

From 9a93d9c7b364533043a24d496697f2fbe5d0aa49 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 11:10:22 -0700
Subject: [PATCH 27/61] Release notes

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index d4b549e0..58b7bc70 100644
--- a/README.md
+++ b/README.md
@@ -26,6 +26,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Remove `cleanOut` task defined by `FileModule` plugin
 - Remove `cleanAndDeploy` task from `ServerDeploy` plugin
 - Update `CopyAndInstallRPackage` Task class to use injected FileSystem instead of `project.copy`
+- Update `GzipAction` task to use task logger and ant builder objects
 
 ### 6.3.0
 *Released*: 3 July 2025

From 34646cf500966f7c50bdec81686b087a63b77973 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 11 Aug 2025 11:36:28 -0700
Subject: [PATCH 28/61] setProjectPath not setProject

---
 .../org/labkey/gradle/plugin/extension/TeamCityExtension.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
index 9ee9b7b0..b8a0b445 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
@@ -89,7 +89,7 @@ class TeamCityExtension
         }
         DatabaseProperties props = new DatabaseProperties(typeAndVersion, typeName, null)
 
-        props.setProject(project)
+        props.setProjectPath(project.path)
         props.jdbcDatabase = getDatabaseName()
         if (!getTeamCityProperty("database.${typeAndVersion}.jdbcURL").isEmpty())
         {

From 7fd3753ee765087fc43843c52f85b47a8bd41104 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 12 Aug 2025 09:31:29 -0700
Subject: [PATCH 29/61] Remove some more deprecated tasks. Update DeployApp
 with proper trigger file configuration. Update StopLabKey properties and
 conditions

---
 README.md                                     |  2 ++
 .../labkey/gradle/plugin/ServerDeploy.groovy  | 21 ++++--------
 .../org/labkey/gradle/plugin/TeamCity.groovy  |  2 +-
 .../org/labkey/gradle/plugin/Tomcat.groovy    | 16 ++-------
 .../extension/DistributionExtension.groovy    |  3 +-
 .../extension/ServerDeployExtension.groovy    | 17 ++++++----
 .../plugin/extension/TeamCityExtension.groovy |  2 +-
 .../org/labkey/gradle/task/DeployApp.groovy   | 28 +++++++++++++--
 .../org/labkey/gradle/task/DoThenSetup.groovy | 10 +++---
 .../org/labkey/gradle/task/StartLabKey.groovy | 34 ++++++++++++-------
 .../org/labkey/gradle/task/StopLabKey.groovy  |  9 +++--
 .../gradle/task/TeamCityPropertiesTask.groovy | 14 +++++++-
 .../org/labkey/gradle/util/BuildUtils.groovy  | 23 +++++++------
 13 files changed, 109 insertions(+), 72 deletions(-)

diff --git a/README.md b/README.md
index 58b7bc70..86544130 100644
--- a/README.md
+++ b/README.md
@@ -27,6 +27,8 @@ on how to do that, including how to develop and test locally and the versioning
 - Remove `cleanAndDeploy` task from `ServerDeploy` plugin
 - Update `CopyAndInstallRPackage` Task class to use injected FileSystem instead of `project.copy`
 - Update `GzipAction` task to use task logger and ant builder objects
+- Remove deprecated `StopTomcat` and `StartTomcat` in favor of `StopLabKey` and `StartLabKey`, repsectively
+- Remove deprecated `getServerDeployDirectory` from `ServerDeployExtension`
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index c7e07806..138ca41b 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -62,7 +62,7 @@ class ServerDeploy implements Plugin<Project>
         serverDeploy = project.extensions.create("serverDeploy", ServerDeployExtension)
 
         deployDir = ServerDeployExtension.getServerDeployDirectoryPath(project)
-        embeddedDir = ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)
+        embeddedDir = ServerDeployExtension.getEmbeddedServerDeployDirectory(project).getAsFile().getAbsolutePath()
         stagingDir = BuildUtils.getRootBuildDirFile(project, STAGING_DIR)
 
         project.apply plugin: 'org.labkey.build.base'
@@ -91,7 +91,7 @@ class ServerDeploy implements Plugin<Project>
                 task.group = GroupNames.DEPLOY
                 task.description = "Deploy the application locally into ${deployDir}"
                 task.binaries.setFrom(project.configurations.binaries)
-                task.notCompatibleWithConfigurationCache("TODO 'cannot serialize project' error, but unclear where it comes from")
+                task.bootJar.setFrom(project.project(BuildUtils.getEmbeddedProjectPath()).tasks.bootJar)
         }
 
         project.tasks.register("stageModules", StageModules) {
@@ -148,6 +148,7 @@ class ServerDeploy implements Plugin<Project>
                             linkBinaries(project, "npm", project.npmVersion, project.npmWorkDirectory)
                     })
                     task.dependsOn(project.tasks.npmSetup)
+                    task.notCompatibleWithConfigurationCache("Needs its own class to declare proper input and output properties")
             }
             project.tasks.symlinkNode.notCompatibleWithConfigurationCache("References project properties. Need to add task class with input properties")
             project.tasks.named('deployApp').configure {dependsOn(project.tasks.symlinkNode)}
@@ -216,16 +217,8 @@ class ServerDeploy implements Plugin<Project>
                         delete.delete embeddedDir
                     }
             }
-            project.tasks.named('deployApp').configure {
-                mustRunAfter(project.tasks.cleanEmbeddedDeploy)
-                doLast {
-                    project.copy {
-                        CopySpec copy ->
-                            copy.from embeddedProject.tasks.bootJar
-                            copy.into embeddedDir
-                            copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
-                    }
-                }
+            project.tasks.named('deployApp').configure {Task task ->
+                task.mustRunAfter(project.tasks.cleanEmbeddedDeploy)
             }
             TaskUtils.getOptionalTask(embeddedProject, 'checkVersionConflicts').ifPresent(task -> {
                 project.tasks.named('deployApp').configure {dependsOn(task)}
@@ -292,10 +285,10 @@ class ServerDeploy implements Plugin<Project>
         project.tasks.named('deployApp').configure {mustRunAfter(project.tasks.cleanBuild)}
 
         project.tasks.named("cleanBuild").configure {
-            it.dependsOn(project.tasks.stopTomcat)
+            it.dependsOn(project.tasks.stopLabKey)
         }
         project.tasks.named("cleanDeploy").configure {
-            it.dependsOn(project.tasks.stopTomcat)
+            it.dependsOn(project.tasks.stopLabKey)
         }
     }
 
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index ea1ccc14..679a5949 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -116,7 +116,7 @@ class TeamCity extends Tomcat
                 }
         }
 
-        project.tasks.named("stopTomcat").configure {
+        project.tasks.named("stopLabKey").configure {
             it.doLast {
                 ensureShutdown(it.logger)
             }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy b/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
index 4383d899..45feb903 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
@@ -25,6 +25,7 @@ import org.labkey.gradle.plugin.extension.TomcatExtension
 import org.labkey.gradle.plugin.extension.UiTestExtension
 import org.labkey.gradle.task.StartLabKey
 import org.labkey.gradle.task.StopLabKey
+import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 
 /**
@@ -59,27 +60,16 @@ class Tomcat implements Plugin<Project>
                 task.description = "Start the LabKey web application"
         }
 
-        project.tasks.register("startTomcat", StartLabKey) {
-            StartLabKey task ->
-                task.group = GroupNames.WEB_APPLICATION
-                task.description = "Start the LabKey web application (deprecated: use startLabKey)"
-        }
-
         project.tasks.register("stopLabKey", StopLabKey) {
             StopLabKey task ->
                 task.group = GroupNames.WEB_APPLICATION
                 task.description = "Stop the LabKey web application"
-        }
-
-        project.tasks.register("stopTomcat", StopLabKey) {
-            StopLabKey task ->
-                task.group = GroupNames.WEB_APPLICATION
-                task.description = "Stop the LabKey web application (deprecated: use stopLabKey)"
+                task.onlyIf{ BuildUtils.getApplicationPropertiesFile(project).exists() }
         }
 
         project.tasks.register("cleanLogs", Delete) {
             Delete task ->
-                var logDir = "${ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)}/logs"
+                var logDir = ServerDeployExtension.getEmbeddedServerDeployDirectory(project).dir("logs")
                 task.group = GroupNames.WEB_APPLICATION
                 task.description = "Delete logs from ${logDir}"
                 task.configure { DeleteSpec spec -> spec.delete project.fileTree(logDir) }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
index 4e8e56bb..02a2c206 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
@@ -28,8 +28,7 @@ class DistributionExtension
     public static final String TAR_ARCHIVE_EXTENSION = "tar.gz"
 
     String dir = "${project.rootProject.projectDir}/dist"
-    String artifactId
-    String description
+    String description // TODO this is set in various distribution build.gradle files but doesn't seem to be used. Remove?
 
     private Project project
 
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/ServerDeployExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/ServerDeployExtension.groovy
index 5f91aa2a..85b94a56 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/ServerDeployExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/ServerDeployExtension.groovy
@@ -17,22 +17,27 @@ package org.labkey.gradle.plugin.extension
 
 import org.gradle.api.Project
 import org.gradle.api.file.Directory
+import org.gradle.api.provider.Provider
 import org.labkey.gradle.plugin.ServerDeploy
 import org.labkey.gradle.util.BuildUtils
 
 class ServerDeployExtension
 {
-    Map<String, String> foundModules = new HashMap<>();
+    Map<String, String> foundModules = new HashMap<>()
 
-    @Deprecated(forRemoval=true)
-    static String getServerDeployDirectory(Project project)
+    static String getServerDeployDirectoryPath(Project project)
     {
-        return getServerDeployDirectoryPath(project)
+        return BuildUtils.getRootBuildDirFile(project, ServerDeploy.DEPLOY_DIR).path
     }
 
-    static String getServerDeployDirectoryPath(Project project)
+    static Provider<Directory> getServerDeployDirectoryProvider(Project project)
     {
-        return BuildUtils.getRootBuildDirFile(project, ServerDeploy.DEPLOY_DIR).path
+        return BuildUtils.getRootBuildDirectoryProvider(project, ServerDeploy.DEPLOY_DIR)
+    }
+
+    static Directory getEmbeddedServerDeployDirectory(Project project)
+    {
+        return getServerDeployDirectoryProvider(project).get().dir("embedded")
     }
 
     static String getEmbeddedServerDeployDirectoryPath(Project project)
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
index b8a0b445..dabc8604 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
@@ -116,7 +116,7 @@ class TeamCityExtension
     }
 
     File startupPropertiesDir() {
-        File startupDir = new File(new File(ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)), 'startup')
+        File startupDir = ServerDeployExtension.getEmbeddedServerDeployDirectory(project).dir('startup').asFile
         FileUtils.forceMkdir(startupDir)
         return startupDir
     }
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
index a0f0a5ab..d1d16dd2 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
@@ -15,15 +15,20 @@
  */
 package org.labkey.gradle.task
 
+import org.gradle.api.file.ConfigurableFileCollection
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
+import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.OutputDirectory
+import org.gradle.api.tasks.OutputFile
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.ServerDeploy
+import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.util.BuildUtils
 
 abstract class DeployApp extends DeployAppBase
@@ -50,8 +55,14 @@ abstract class DeployApp extends DeployAppBase
     @Input
     final abstract Property<Boolean> useLocalBuild = project.objects.property(Boolean).convention(project.hasProperty("useLocalBuild") && "false" != project.property("useLocalBuild"))
 
-    @InputDirectory
-    File restartTriggerFileDir = BuildUtils.getTriggerFileDir(project)
+    @OutputFile
+    final abstract RegularFileProperty restartTriggerFile = project.objects.fileProperty().fileValue(BuildUtils.getRestartTriggerFile(project))
+
+    @OutputDirectory
+    final abstract DirectoryProperty embeddedDir = project.objects.directoryProperty().convention(ServerDeployExtension.getEmbeddedServerDeployDirectory(project))
+
+    @InputFiles
+    abstract ConfigurableFileCollection getBootJar()
 
     @TaskAction
     void action()
@@ -59,7 +70,8 @@ abstract class DeployApp extends DeployAppBase
         deployModules()
         deployPipelineJars()
         deployPlatformBinaries(deployBinDir.get().asFile)
-        BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFileDir)
+        deployEmbeddedBootJar()
+        BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
     }
 
     private void deployModules()
@@ -81,4 +93,14 @@ abstract class DeployApp extends DeployAppBase
             copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
         })
     }
+
+    private void deployEmbeddedBootJar()
+    {
+        fs.copy {
+            CopySpec copy ->
+                copy.from bootJar
+                copy.into embeddedDir.get()
+                copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
+        }
+    }
 }
diff --git a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
index 71c3a71a..95e03fd9 100644
--- a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
@@ -28,6 +28,7 @@ import org.gradle.api.tasks.InputDirectory
 import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.Optional
+import org.gradle.api.tasks.OutputFile
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
@@ -37,9 +38,6 @@ import javax.inject.Inject
 import java.sql.Driver
 import java.sql.DriverManager
 
-// TODO making this extend from RestartTriggerTask causes the following error on TeamCity:
-//  Cannot fingerprint input property 'databaseProperties': value 'org.labkey.gradle.util.DatabaseProperties@286cb41a' cannot be serialized.
-// Even though RestartTriggerTask has nothing to do with the `databaseProperties`
 abstract class DoThenSetup extends TeamCityPropertiesTask
 {
     // TODO rethink this input declaration. Dependence on a file makes more sense
@@ -73,8 +71,8 @@ abstract class DoThenSetup extends TeamCityPropertiesTask
     @InputDirectory
     File configsDir = new File(BuildUtils.getConfigsProject(project).projectDir, "configs")
 
-    @InputDirectory
-    File restartTriggerFileDir = BuildUtils.getTriggerFileDir(project)
+    @OutputFile
+    final abstract RegularFileProperty restartTriggerFile = project.objects.fileProperty().fileValue(BuildUtils.getRestartTriggerFile(project))
 
     @Inject abstract FileSystemOperations getFs()
 
@@ -131,7 +129,7 @@ abstract class DoThenSetup extends TeamCityPropertiesTask
                     return PropertiesUtils.replaceProps(line, configProperties, false)
                 })
             })
-            BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFileDir)
+            BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
         }
     }
 
diff --git a/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy b/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
index aa0e7a70..2132e219 100644
--- a/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
@@ -17,9 +17,12 @@ package org.labkey.gradle.task
 
 import org.apache.commons.lang3.StringUtils
 import org.apache.commons.lang3.SystemUtils
-import org.gradle.api.DefaultTask
 import org.gradle.api.GradleException
 import org.gradle.api.Project
+import org.gradle.api.file.DirectoryProperty
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.OutputFile
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.Tomcat
 import org.labkey.gradle.plugin.extension.LabKeyExtension
@@ -28,7 +31,7 @@ import org.labkey.gradle.util.BuildUtils
 
 import java.util.stream.Collectors
 
-class StartLabKey extends DefaultTask
+abstract class StartLabKey extends TeamCityPropertiesTask
 {
     private static final String EMBEDDED_REFLECTION_PARAM = "embeddedReflectionArgs"
     private static final List<String> DEFAULT_EMBEDDED_REFLECTION_OPTS = [
@@ -40,17 +43,23 @@ class StartLabKey extends DefaultTask
             "--add-opens=java.base/java.text=ALL-UNNAMED"
     ]
 
+    @InputDirectory
+    final abstract DirectoryProperty deployDir = project.objects.directoryProperty().convention(ServerDeployExtension.getEmbeddedServerDeployDirectory(project))
+
+    @OutputFile
+    final abstract RegularFileProperty logFileProp = project.objects.fileProperty().convention(ServerDeployExtension.getEmbeddedServerDeployDirectory(project).file(Tomcat.EMBEDDED_LOG_FILE_NAME))
+
     @TaskAction
     void action()
     {
-        File jarFile = BuildUtils.getExecutableServerJar(project)
+        File jarFile = BuildUtils.getExecutableServerJar(deployDir.get().asFile)
         if (jarFile == null)
         {
-            throw new GradleException("No jar file found in ${ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)}.")
+            throw new GradleException("No jar file found in ${deployDir.get().asFile}.")
         }
         else
         {
-            String javaHome = TeamCityPropertiesTask.getTeamCityProperty(project, "tomcatJavaHome", System.getenv("JAVA_HOME"))
+            String javaHome = tomcatJavaHome.get()
             if (StringUtils.isEmpty(javaHome))
                 throw new GradleException("JAVA_HOME must be set in order to start your embedded tomcat server.")
             File javaBin = new File(javaHome, "bin")
@@ -62,20 +71,21 @@ class StartLabKey extends DefaultTask
             commandParts += getStartupOpts(project)
             commandParts += ["-jar", jarFile.getName()]
 
-            File logFile = new File(ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project), Tomcat.EMBEDDED_LOG_FILE_NAME)
+            File logFile = logFileProp.get().asFile
             if (!logFile.getParentFile().exists())
                 logFile.getParentFile().mkdirs()
             if (!logFile.exists())
                 logFile.createNewFile()
             FileOutputStream outputStream = new FileOutputStream(logFile)
             def envMap = new HashMap<>(System.getenv())
-            envMap.put('PATH', "${ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)}/bin${File.pathSeparator}${System.getenv("PATH")}")
+            String deployDirPath = deployDir.get().asFile.getAbsolutePath()
+            envMap.put('PATH', "${deployDirPath}/bin${File.pathSeparator}${System.getenv("PATH")}")
             def env = []
             for (String key : envMap.keySet()) {
                 env += "${key}=${envMap.get(key)}"
             }
-            this.logger.info("Starting LabKey with command ${commandParts} and env ${env} in directory ${ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)}")
-            Process process = commandParts.execute(env, new File(ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project)))
+            this.logger.info("Starting LabKey with command ${commandParts} and env ${env} in directory ${deployDirPath}")
+            Process process = commandParts.execute(env, deployDir.get().asFile)
             process.consumeProcessOutput(outputStream, outputStream)
         }
     }
@@ -86,7 +96,7 @@ class StartLabKey extends DefaultTask
         optsList.add(project.tomcat.assertionFlag)
         optsList.add("-Ddevmode=${LabKeyExtension.isDevMode(project)}".toString())
         optsList.addAll(project.tomcat.catalinaOpts.split(" "))
-        optsList.add("-Xmx${TeamCityPropertiesTask.getTeamCityProperty(project, "Xmx", project.tomcat.maxMemory)}".toString())
+        optsList.add("-Xmx${getTeamCityProperty(project, "Xmx", project.tomcat.maxMemory)}".toString())
         if (project.tomcat.disableRecompileJsp)
             optsList.add("-Dlabkey.disableRecompileJsp=true")
         if (project.tomcat.ignoreModuleSource)
@@ -94,9 +104,9 @@ class StartLabKey extends DefaultTask
         optsList.add(project.tomcat.trustStore)
         optsList.add(project.tomcat.trustStorePassword)
 
-        if (TeamCityPropertiesTask.isOnTeamCity(project) && SystemUtils.IS_OS_UNIX)
+        if (isOnTeamCity(project) && SystemUtils.IS_OS_UNIX)
         {
-            optsList.add("-DsequencePipelineEnabled=${TeamCityPropertiesTask.getTeamCityProperty(project, "sequencePipelineEnabled", false)}".toString())
+            optsList.add("-DsequencePipelineEnabled=${getTeamCityProperty(project, "sequencePipelineEnabled", false)}".toString())
         }
 
         if (project.hasProperty("extraCatalinaOpts"))
diff --git a/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy b/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
index 86ef8b0a..f0477966 100644
--- a/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StopLabKey.groovy
@@ -16,6 +16,7 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFile
@@ -29,7 +30,9 @@ import org.labkey.gradle.util.BuildUtils
 class StopLabKey extends DefaultTask
 {
     @InputFile
-    File propertiesFile = BuildUtils.getApplicationPropertiesFile(project)
+    final abstract RegularFileProperty propertiesFile = project.objects.fileProperty().fileValue(
+            BuildUtils.getApplicationPropertiesFile(project)
+    )
 
     @Input
     final abstract Property<Boolean> useSsl = project.objects.property(Boolean).convention(project.hasProperty("useSsl"))
@@ -37,9 +40,9 @@ class StopLabKey extends DefaultTask
     @TaskAction
     void action()
     {
-        def applicationProperties = PropertiesUtils.getApplicationProperties(propertiesFile)
+        def applicationProperties = PropertiesUtils.getApplicationProperties(propertiesFile.get().asFile)
         def port = applicationProperties.getProperty("management.server.port", applicationProperties.getProperty("server.port"))
-        def endpoint =  "${useSsl.get() ? "https" : "http"}://localhost:$port/actuator/shutdown"
+        def endpoint = "${useSsl.get() ? "https" : "http"}://localhost:$port/actuator/shutdown"
         def command = "curl -X POST $endpoint"
         this.logger.info("Sending command to $endpoint")
         def proc = command.execute()
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
index 4edaf05d..8b76308e 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
@@ -52,7 +52,14 @@ abstract class TeamCityPropertiesTask extends DefaultTask
     @Optional @Input
     final abstract Property<String> labKeyServer = project.objects.property(String).convention(getLabKeyServer(project))
 
-
+    @Optional @Input
+    final abstract Property<String> tomcatJavaHome = project.objects.property(String).convention(
+            tcPropOrDefault(project,
+                TeamCityPropertiesTask::getTomcatJavaHome,
+                    "tomcatJavaHome",
+                    System.getenv("JAVA_HOME")
+            )
+    )
 
     protected static String tcPropOrDefault(Project project, Function<Project, String> tcPropertyFunc, String projectPropertyName, String defaultValue)
     {
@@ -132,4 +139,9 @@ abstract class TeamCityPropertiesTask extends DefaultTask
     {
         return getTeamCityProperty(project, "labkey.server.password", "We'reSo\$tr0ng@yekbal1!")
     }
+
+    static String getTomcatJavaHome(Project project)
+    {
+        return getTeamCityProperty(project, "tomcatJavaHome", System.getenv("JAVA_HOME"))
+    }
 }
diff --git a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
index c441af9b..5abeed3a 100644
--- a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
@@ -849,12 +849,16 @@ class BuildUtils
 
     static String getEmbeddedConfigPath(Project project)
     {
-        return new File(ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project), "config").absolutePath
+        return getEmbeddedConfigDirectory(project).asFile.absolutePath
     }
 
-    static File getExecutableServerJar(Project project)
+    static Directory getEmbeddedConfigDirectory(Project project)
+    {
+        return ServerDeployExtension.getEmbeddedServerDeployDirectory(project).dir("config")
+    }
+
+    static File getExecutableServerJar(File deployDir)
     {
-        File deployDir = new File(ServerDeployExtension.getEmbeddedServerDeployDirectoryPath(project))
         File[] jarFiles = deployDir.listFiles(new FilenameFilter() {
             @Override
             boolean accept(File dir, String name) {
@@ -886,25 +890,24 @@ class BuildUtils
      */
     static void updateRestartTriggerFile(Project project)
     {
-        updateRestartTriggerFile(project.hasProperty('useLocalBuild') && "false" != project.property("useLocalBuild"), getTriggerFileDir(project))
+        updateRestartTriggerFile(project.hasProperty('useLocalBuild') && "false" != project.property("useLocalBuild"), getRestartTriggerFile(project))
     }
 
-    static File getTriggerFileDir(Project project)
+    static File getRestartTriggerFile(Project project)
     {
-        return project.rootProject.layout.buildDirectory.file("deploy/modules").get().getAsFile()
+        return project.rootProject.layout.buildDirectory.file("deploy/modules/" + RESTART_FILE_NAME).get().getAsFile()
     }
 
-    static void updateRestartTriggerFile(boolean useLocalBuild, File triggerFileDir)
+    static void updateRestartTriggerFile(boolean useLocalBuild, File triggerFile)
     {
         if (!useLocalBuild)
             return
 
-        if (!triggerFileDir.exists())
-            return
+        if (!triggerFile.getParentFile().exists())
+            triggerFile.getParentFile().mkdirs()
 
         OutputStreamWriter writer = null
         try {
-            File triggerFile = new File(triggerFileDir, RESTART_FILE_NAME)
             writer = new OutputStreamWriter(new FileOutputStream(triggerFile), StandardCharsets.UTF_8)
             writer.write(SimpleDateFormat.getDateTimeInstance().format(new Date()))
         }

From 32748587979a27169e73df77e0ba18601d6ab331 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 12 Aug 2025 11:40:53 -0700
Subject: [PATCH 30/61] startTomcat -> startLabKey

---
 .../org/labkey/gradle/plugin/TeamCity.groovy     | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 679a5949..a3700231 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -150,7 +150,7 @@ class TeamCity extends Tomcat
             }
         }
 
-        project.tasks.named("startTomcat").configure {
+        project.tasks.named("startLabKey").configure {
             dependsOn(project.tasks.createStartupPropertyFile)
         }
 
@@ -176,7 +176,7 @@ class TeamCity extends Tomcat
 
         }
 
-        project.tasks.named("startTomcat").configure {
+        project.tasks.named("startLabKey").configure {
             dependsOn(project.tasks.createNlpConfig)
         }
 
@@ -247,11 +247,11 @@ class TeamCity extends Tomcat
                 }
             }
             undeployTask = project.tasks.named(undeployTaskName)
-            project.tasks.named("startTomcat").configure {
+            project.tasks.named("startLabKey").configure {
                 mustRunAfter(undeployTask)
             }
 
-            project.project(BuildUtils.getTestProjectPath(project.gradle)).tasks.startTomcat.mustRunAfter(setUpDbTask)
+            project.project(BuildUtils.getTestProjectPath(project.gradle)).tasks.startLabKey.mustRunAfter(setUpDbTask)
             String ciTestTaskName = "ciTests" + properties.dbTypeAndVersion.capitalize()
             project.tasks.register(ciTestTaskName, RunTestSuite) {
                 RunTestSuite task ->
@@ -261,7 +261,7 @@ class TeamCity extends Tomcat
                     task.dbProperties = properties
                     task.mustRunAfter(project.tasks.validateConfiguration)
                     task.mustRunAfter(project.tasks.cleanTestLogs)
-                    task.mustRunAfter(project.tasks.startTomcat)
+                    task.mustRunAfter(project.tasks.startLabKey)
             }
 
             ciTests.add(project.tasks.named(ciTestTaskName))
@@ -290,7 +290,7 @@ class TeamCity extends Tomcat
                     }
             }
 
-            project.tasks.named("startTomcat").configure {
+            project.tasks.named("startLabKey").configure {
                 dependsOn(includeDistModulesTask)
             }
         }
@@ -299,7 +299,7 @@ class TeamCity extends Tomcat
             Task task ->
                 task.group = GroupNames.TEST_SERVER
                 task.dependsOn( ciTests )
-                task.dependsOn( project.tasks.validateConfiguration, project.tasks.startTomcat, project.tasks.cleanTestLogs)
+                task.dependsOn( project.tasks.validateConfiguration, project.tasks.startLabKey, project.tasks.cleanTestLogs)
                 task.description = "Run a test suite on the TeamCity server"
                 task.doLast(
              {
@@ -307,7 +307,7 @@ class TeamCity extends Tomcat
                     }
                 )
         }
-        project.tasks.named("startTomcat").configure {
+        project.tasks.named("startLabKey").configure {
             mustRunAfter(project.tasks.cleanTestLogs)
         }
     }

From 9b02224f02b4d7b89e239578158f15986158d131 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 06:58:44 -0700
Subject: [PATCH 31/61] Restore startTomcat and stopTomcat; remove
 `createNlpConfig` task

---
 .../org/labkey/gradle/plugin/TeamCity.groovy  | 48 +++++++------------
 .../org/labkey/gradle/plugin/Tomcat.groovy    | 13 +++++
 2 files changed, 29 insertions(+), 32 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index a3700231..2467fd23 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -15,7 +15,6 @@
  */
 package org.labkey.gradle.plugin
 
-
 import com.sun.jdi.AbsentInformationException
 import com.sun.jdi.Bootstrap
 import com.sun.jdi.IncompatibleThreadStateException
@@ -36,11 +35,9 @@ import org.gradle.api.UnknownTaskException
 import org.gradle.api.file.DeleteSpec
 import org.gradle.api.logging.Logger
 import org.gradle.api.provider.Provider
-import org.gradle.api.tasks.Copy
 import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.JavaExec
 import org.gradle.api.tasks.TaskProvider
-import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.PickDb
 import org.labkey.gradle.task.RunTestSuite
@@ -50,10 +47,8 @@ import org.labkey.gradle.task.UndeployModules
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.GroupNames
-import org.labkey.gradle.util.PropertiesUtils
 
 import java.time.Duration
-import java.util.regex.Matcher
 
 /**
  * Creates tasks for TeamCity to run its tests suites based on properties set in a build configuration (particularly for
@@ -63,7 +58,6 @@ class TeamCity extends Tomcat
 {
     private static final String TEAMCITY_INFO_FILE = "teamcity-info.xml"
     private static final String TEST_CONFIGS_DIR = "configs/config-test"
-    private static final String NLP_CONFIG_FILE = "nlpConfig.xml"
     private static final String PIPELINE_CONFIG_FILE =  "pipelineConfig.xml"
     private static final Duration TOMCAT_SHUTDOWN_TIMEOUT = Duration.ofSeconds(15)
 
@@ -122,6 +116,12 @@ class TeamCity extends Tomcat
             }
         }
 
+        project.tasks.named("stopTomcat").configure {
+            it.doLast {
+                ensureShutdown(it.logger)
+            }
+        }
+
         project.tasks.register("killChrome") {
             Task task ->
                 task.group = GroupNames.TEST_SERVER
@@ -154,30 +154,8 @@ class TeamCity extends Tomcat
             dependsOn(project.tasks.createStartupPropertyFile)
         }
 
-        project.tasks.register("createNlpConfig", Copy) {
-            Copy task ->
-                task.group = GroupNames.TEST_SERVER
-                task.description = "Create NLP engine configs for the test server"
-                task.from BuildUtils.getServerProject(project).file(TEST_CONFIGS_DIR)
-                task.include NLP_CONFIG_FILE
-                task.inputs.property("directoryPath", new File((String) project.labkey.externalDir, "nlp/nlp_engine.py").getAbsolutePath())
-                task.filter({ String line ->
-                    Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
-                    String newLine = line
-                    while (matcher.find())
-                    {
-                        if (matcher.group(1).equals("enginePath"))
-                            newLine = newLine.replace(matcher.group(), (String) task.inputs.properties.get("directoryPath"))
-                    }
-                    return newLine
-                }
-                )
-                task.destinationDir = new File("${ServerDeployExtension.getServerDeployDirectoryPath(project)}/config")
-
-        }
-
-        project.tasks.named("startLabKey").configure {
-            dependsOn(project.tasks.createNlpConfig)
+        project.tasks.named("startTomcat").configure {
+            dependsOn(project.tasks.createStartupPropertyFile)
         }
 
         project.tasks.register("validateConfiguration") {
@@ -291,7 +269,10 @@ class TeamCity extends Tomcat
             }
 
             project.tasks.named("startLabKey").configure {
-                dependsOn(includeDistModulesTask)
+                it.dependsOn(includeDistModulesTask)
+            }
+            project.tasks.named("startTomcat").configure {
+                it.dependsOn(includeDistModulesTask)
             }
         }
 
@@ -308,7 +289,10 @@ class TeamCity extends Tomcat
                 )
         }
         project.tasks.named("startLabKey").configure {
-            mustRunAfter(project.tasks.cleanTestLogs)
+            it.mustRunAfter(project.tasks.cleanTestLogs)
+        }
+        project.tasks.named("startTomcat").configure {
+            it.mustRunAfter(project.tasks.cleanTestLogs)
         }
     }
 
diff --git a/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy b/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
index 45feb903..63c4814d 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
@@ -67,6 +67,19 @@ class Tomcat implements Plugin<Project>
                 task.onlyIf{ BuildUtils.getApplicationPropertiesFile(project).exists() }
         }
 
+        project.tasks.register("startTomcat", StartLabKey) {
+            StartLabKey task ->
+                task.group = GroupNames.WEB_APPLICATION
+                task.description = "Start the LabKey web application (deprecated: use startLabKey)"
+        }
+
+        project.tasks.register("stopTomcat", StopLabKey) {
+            StopLabKey task ->
+                task.group = GroupNames.WEB_APPLICATION
+                task.description = "Stop the LabKey web application (deprecated: use stopLabKey)"
+                task.onlyIf{ BuildUtils.getApplicationPropertiesFile(project).exists() }
+        }
+
         project.tasks.register("cleanLogs", Delete) {
             Delete task ->
                 var logDir = ServerDeployExtension.getEmbeddedServerDeployDirectory(project).dir("logs")

From 2a97191a020e19b104c90a2c1ee4a77637f26030 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 09:20:31 -0700
Subject: [PATCH 32/61] Remove explicit `setup` task and fix up tasks that were
 depending on it incorrectly

---
 README.md                                     |   4 +-
 .../labkey/gradle/plugin/ServerDeploy.groovy  |  86 +++----
 .../org/labkey/gradle/task/DeployApp.groovy   |  11 +-
 .../labkey/gradle/task/DeployAppBase.groovy   |   3 +-
 .../gradle/task/DeployDistribution.groovy     |   1 +
 .../org/labkey/gradle/task/DoThenSetup.groovy | 226 +---------------
 .../labkey/gradle/task/SetUpProperties.groovy | 243 ++++++++++++++++++
 7 files changed, 294 insertions(+), 280 deletions(-)
 create mode 100644 src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy

diff --git a/README.md b/README.md
index 86544130..0cb077a4 100644
--- a/README.md
+++ b/README.md
@@ -27,8 +27,10 @@ on how to do that, including how to develop and test locally and the versioning
 - Remove `cleanAndDeploy` task from `ServerDeploy` plugin
 - Update `CopyAndInstallRPackage` Task class to use injected FileSystem instead of `project.copy`
 - Update `GzipAction` task to use task logger and ant builder objects
-- Remove deprecated `StopTomcat` and `StartTomcat` in favor of `StopLabKey` and `StartLabKey`, repsectively
+- Update `StopLabKey` and `StartLabKey` with appropriate dependencies to mirror the deprecated `StopTomcat` and `StartTomcat`
 - Remove deprecated `getServerDeployDirectory` from `ServerDeployExtension`
+- TODO Remove `createNlpConfig` task from `TeamCity` plugin since that module is no longer in use
+- Remove `setup` task from `ServerDeploy` plugin.
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index 138ca41b..2e502db9 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -86,13 +86,7 @@ class ServerDeploy implements Plugin<Project>
 
     private void addTasks(Project project)
     {
-        project.tasks.register("deployApp", DeployApp) {
-            DeployApp task ->
-                task.group = GroupNames.DEPLOY
-                task.description = "Deploy the application locally into ${deployDir}"
-                task.binaries.setFrom(project.configurations.binaries)
-                task.bootJar.setFrom(project.project(BuildUtils.getEmbeddedProjectPath()).tasks.bootJar)
-        }
+
 
         project.tasks.register("stageModules", StageModules) {
             StageModules task ->
@@ -127,32 +121,6 @@ class ServerDeploy implements Plugin<Project>
                 task.dependsOn(project.tasks.checkModuleVersions)
         }
 
-        // Creating symbolic links on Windows requires elevated permissions.  Even with these permissions, the createSymbolicLink method fails
-        // with a message "required privilege is not held by the client".  Using the ant.symlink task "succeeds", but it causes .sys files to be created in the
-        // .node directory, which are not symbolic links and will cause failures with a message "java.nio.file.NotLinkException: The file or directory is not a reparse point."
-        // the next time the command is run.
-        //
-        // So, for now, for Windows users, the symbolic links can be created manually using the following command when running as an administrator
-        //   MKLINK /D <npmLinkPath> <npmTargetPath>
-        // or users can skip the link creation and put the target of the link in their path instead.
-        //
-        // At a later date, we can possibly make this task execute the mklink command (and its counterpart to remove the link).
-        // This would require that the gradle tasks be run as an administrator, and that is possibly not ideal.
-        if (!SystemUtils.IS_OS_WINDOWS &&  project.hasProperty('nodeVersion')) {
-            project.tasks.register("symlinkNode") {
-                Task task ->
-                    task.group = GroupNames.DEPLOY
-                    task.description = "Make a symbolic link to the npm directory for use in PATH environment variable"
-                    task.doFirst({
-                        if (project.hasProperty('npmVersion') && project.hasProperty('npmWorkDirectory'))
-                            linkBinaries(project, "npm", project.npmVersion, project.npmWorkDirectory)
-                    })
-                    task.dependsOn(project.tasks.npmSetup)
-                    task.notCompatibleWithConfigurationCache("Needs its own class to declare proper input and output properties")
-            }
-            project.tasks.symlinkNode.notCompatibleWithConfigurationCache("References project properties. Need to add task class with input properties")
-            project.tasks.named('deployApp').configure {dependsOn(project.tasks.symlinkNode)}
-        }
 
         String stagingPipelineLibDir = BuildUtils.getRootBuildDirFile(project, STAGING_PIPELINE_DIR)
 
@@ -191,21 +159,45 @@ class ServerDeploy implements Plugin<Project>
                 task.dependsOn project.tasks.stageRemotePipelineJars
         }
 
-        project.tasks.register(
-                "setup",  DoThenSetup) {
-            DoThenSetup task ->
+        project.tasks.register("deployApp", DeployApp) {
+            DeployApp task ->
                 task.group = GroupNames.DEPLOY
-                task.description = "Installs application.properties into the tomcat configuration directory. Sets default database properties."
+                task.description = "Deploy the application locally into ${deployDir}"
+                task.binaries.setFrom(project.configurations.binaries)
+                task.bootJar.setFrom(project.project(BuildUtils.getEmbeddedProjectPath()).tasks.bootJar)
                 task.driverFiles.setFrom(project.configurations.driver)
                 // stage the application first to try to avoid multiple Tomcat restarts
-                task.mustRunAfter(project.tasks.stageApp)
+                task.dependsOn(project.tasks.stageApp)
         }
 
-        project.tasks.named('deployApp').configure {
-            dependsOn(project.tasks.setup)
-            dependsOn(project.tasks.stageApp)
+        // Creating symbolic links on Windows requires elevated permissions.  Even with these permissions, the createSymbolicLink method fails
+        // with a message "required privilege is not held by the client".  Using the ant.symlink task "succeeds", but it causes .sys files to be created in the
+        // .node directory, which are not symbolic links and will cause failures with a message "java.nio.file.NotLinkException: The file or directory is not a reparse point."
+        // the next time the command is run.
+        //
+        // So, for now, for Windows users, the symbolic links can be created manually using the following command when running as an administrator
+        //   MKLINK /D <npmLinkPath> <npmTargetPath>
+        // or users can skip the link creation and put the target of the link in their path instead.
+        //
+        // At a later date, we can possibly make this task execute the mklink command (and its counterpart to remove the link).
+        // This would require that the gradle tasks be run as an administrator, and that is possibly not ideal.
+        if (!SystemUtils.IS_OS_WINDOWS &&  project.hasProperty('nodeVersion')) {
+            project.tasks.register("symlinkNode") {
+                Task task ->
+                    task.group = GroupNames.DEPLOY
+                    task.description = "Make a symbolic link to the npm directory for use in PATH environment variable"
+                    task.doFirst({
+                        if (project.hasProperty('npmVersion') && project.hasProperty('npmWorkDirectory'))
+                            linkBinaries(project, "npm", project.npmVersion, project.npmWorkDirectory)
+                    })
+                    task.dependsOn(project.tasks.npmSetup)
+                    task.notCompatibleWithConfigurationCache("Needs its own class to declare proper input and output properties")
+            }
+            project.tasks.symlinkNode.notCompatibleWithConfigurationCache("References project properties. Need to add task class with input properties")
+            project.tasks.named('deployApp').configure {dependsOn(project.tasks.symlinkNode)}
         }
 
+
         if (BuildUtils.embeddedProjectExists(project)) {
             def embeddedProject = project.project(BuildUtils.getEmbeddedProjectPath())
 
@@ -221,11 +213,10 @@ class ServerDeploy implements Plugin<Project>
                 task.mustRunAfter(project.tasks.cleanEmbeddedDeploy)
             }
             TaskUtils.getOptionalTask(embeddedProject, 'checkVersionConflicts').ifPresent(task -> {
-                project.tasks.named('deployApp').configure {dependsOn(task)}
+                project.tasks.named('deployApp').configure {it.dependsOn(task)}
             })
 
-            project.tasks.named('stageApp').configure {dependsOn(embeddedProject.tasks.build)}
-            project.tasks.named('setup').configure {mustRunAfter(project.tasks.cleanEmbeddedDeploy)}
+            project.tasks.named('stageApp').configure {it.dependsOn(embeddedProject.tasks.build)}
 
         }
 
@@ -239,13 +230,10 @@ class ServerDeploy implements Plugin<Project>
             DeployDistribution task ->
                 task.group = GroupNames.DISTRIBUTION
                 task.description = "Extract the executable jar from a distribution and put it and the included binaries in the appropriate deploy directory"
-                task.dependsOn(project.tasks.cleanEmbeddedDeploy, project.tasks.setup)
+                task.dependsOn(project.tasks.cleanEmbeddedDeploy)
                 task.binaries.setFrom(project.configurations.binaries)
         }
 
-        // This may prevent multiple Tomcat restarts
-        project.tasks.named('setup').configure {mustRunAfter(project.tasks.stageDistribution)}
-
         project.tasks.register('undeployModules', UndeployModules) {
             UndeployModules task ->
                 task.group = GroupNames.DEPLOY
@@ -282,7 +270,7 @@ class ServerDeploy implements Plugin<Project>
                     spec.delete project.rootProject.layout.buildDirectory
                 })
         }
-        project.tasks.named('deployApp').configure {mustRunAfter(project.tasks.cleanBuild)}
+        project.tasks.named('deployApp').configure {it.mustRunAfter(project.tasks.cleanBuild)}
 
         project.tasks.named("cleanBuild").configure {
             it.dependsOn(project.tasks.stopLabKey)
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
index d1d16dd2..e3b9a88b 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
@@ -71,18 +71,19 @@ abstract class DeployApp extends DeployAppBase
         deployPipelineJars()
         deployPlatformBinaries(deployBinDir.get().asFile)
         deployEmbeddedBootJar()
+        setUpProperties()
         BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
     }
 
     private void deployModules()
     {
         ant.copy (
-                todir: deployModulesDir.get().asFile,
-                preserveLastModified: true,
+            todir: deployModulesDir.get().asFile,
+            preserveLastModified: true,
         )
-                {
-                    fileset(dir: stagingModulesDir.get().asFile)
-                }
+        {
+            fileset(dir: stagingModulesDir.get().asFile)
+        }
     }
 
     private void deployPipelineJars()
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy b/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
index a22082c9..2f2d86d8 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
@@ -1,7 +1,6 @@
 package org.labkey.gradle.task
 
 import org.apache.commons.lang3.SystemUtils
-import org.gradle.api.DefaultTask
 import org.gradle.api.file.ConfigurableFileCollection
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
@@ -13,7 +12,7 @@ import org.labkey.gradle.util.BuildUtils
 
 import javax.inject.Inject
 
-abstract class DeployAppBase extends DefaultTask {
+abstract class DeployAppBase extends SetUpProperties {
 
     @Inject abstract FileSystemOperations getFs()
 
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy b/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
index a5ffaa7c..1b0543a4 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
@@ -22,6 +22,7 @@ abstract class DeployDistribution extends DeployAppBase {
     {
         deployExecutableJar()
         deployPlatformBinaries(deployBinDir.get().asFile)
+        setUpProperties()
     }
 
     private void deployExecutableJar() {
diff --git a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
index 95e03fd9..22889088 100644
--- a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
@@ -15,67 +15,11 @@
  */
 package org.labkey.gradle.task
 
-import groovy.sql.Sql
-import org.gradle.api.GradleException
-import org.gradle.api.file.ConfigurableFileCollection
-import org.gradle.api.file.CopySpec
-import org.gradle.api.file.DuplicatesStrategy
-import org.gradle.api.file.FileSystemOperations
-import org.gradle.api.file.RegularFileProperty
-import org.gradle.api.provider.Property
-import org.gradle.api.tasks.Input
-import org.gradle.api.tasks.InputDirectory
-import org.gradle.api.tasks.InputFile
-import org.gradle.api.tasks.InputFiles
-import org.gradle.api.tasks.Optional
-import org.gradle.api.tasks.OutputFile
-import org.gradle.api.tasks.TaskAction
-import org.labkey.gradle.util.BuildUtils
-import org.labkey.gradle.util.DatabaseProperties
-import org.labkey.gradle.util.PropertiesUtils
 
-import javax.inject.Inject
-import java.sql.Driver
-import java.sql.DriverManager
+import org.gradle.api.tasks.TaskAction
 
-abstract class DoThenSetup extends TeamCityPropertiesTask
+abstract class DoThenSetup extends SetUpProperties
 {
-    // TODO rethink this input declaration. Dependence on a file makes more sense
-    @Optional @Input
-    protected DatabaseProperties databaseProperties
-
-    @InputFiles
-    abstract ConfigurableFileCollection getDriverFiles()
-
-    @Input
-    boolean dbPropertiesChanged = false
-
-    @InputFile
-    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
-
-    @InputFile
-    final abstract RegularFileProperty applicationPropsFile = project.objects.fileProperty().fileValue(new File(BuildUtils.getEmbeddedConfigPath(project), "application.properties"))
-
-    @Input
-    final abstract Property<Boolean> useSsl = project.objects.property(Boolean).convention(project.hasProperty("useSsl"))
-    @Input
-    final abstract Property<String> portNumber = project.objects.property(String).convention(project.hasProperty("useSsl") ? "8443" : "8080")
-    @Input
-    final abstract Property<Boolean> useLocalBuild = project.objects.property(Boolean).convention(project.hasProperty("useLocalBuild") && "false" != project.property("useLocalBuild"))
-
-    @Input // in .properties files, backward slashes are seen as escape characters, so all paths must use forward slashes, even on Windows
-    final abstract Property<String> pathToServer = project.objects.property(String).convention(project.rootDir.getAbsolutePath().replaceAll("\\\\", "/"))
-
-    @Input
-    final abstract Property<String> embeddedDir = project.objects.property(String).convention(BuildUtils.getEmbeddedConfigPath(project))
-    @InputDirectory
-    File configsDir = new File(BuildUtils.getConfigsProject(project).projectDir, "configs")
-
-    @OutputFile
-    final abstract RegularFileProperty restartTriggerFile = project.objects.fileProperty().fileValue(BuildUtils.getRestartTriggerFile(project))
-
-    @Inject abstract FileSystemOperations getFs()
-
     protected void doDatabaseTask()
     {
         setDatabaseProperties()
@@ -84,170 +28,6 @@ abstract class DoThenSetup extends TeamCityPropertiesTask
     @TaskAction
     void setup() {
         doDatabaseTask()
-        if (!embeddedConfigUpToDate()) {
-            Properties configProperties = databaseProperties.getConfigProperties()
-            configProperties.putAll(getExtraJdbcProperties())
-            configProperties.setProperty("pathToServer", pathToServer.get())
-            configProperties.setProperty("serverPort", labKeyServerPort.get())
-            configProperties.setProperty("contextPath", contextPath.get())
-            configProperties.setProperty("shutdownPort", shutdownPort.get())
-            if (useSsl.get()) {
-                configProperties.setProperty("keyStore", keyStore.get())
-                configProperties.setProperty("keyStorePassword", keyStorePassword.get())
-            }
-
-            fs.copy({ CopySpec copy ->
-                copy.from configsDir
-                copy.into embeddedDir.get()
-                copy.include "application.properties"
-                copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
-                copy.filter({ String line ->
-                    // Always uncomment properties prepended by '#setupTask#'
-                    line = line.replace("#setupTask#", "")
-                    if (useSsl.get()) {
-                        line = line.replace("#server.ssl", "server.ssl")
-                    }
-                    if (useLocalBuild.get()) {
-                        // Enable properties that require 'useLocalBuild' (e.g. 'context.webAppLocation' and 'spring.devtools.restart.additional-paths')
-                        line = line.replace("#useLocalBuild#", "")
-                    }
-                    else {
-                        // Remove placeholder
-                        line = line.replace("#useLocalBuild#", "#")
-                    }
-                    if (configProperties.containsKey("extraJdbcDataSource") && line.contains("=@@extraJdbc"))
-                    {
-                        line = line.replace("#context.", "context.")
-                    }
-                    if (configProperties.containsKey("contextPath") && line.contains("=@@contextPath"))
-                    {
-                        line = line.replace("#context.", "context.")
-                    }
-                    if (line.startsWith("#")) {
-                        return line // Don't apply replacements to comments
-                    }
-                    return PropertiesUtils.replaceProps(line, configProperties, false)
-                })
-            })
-            BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
-        }
-    }
-
-    /**
-     * Get 'extraJdbc*' properties from TeamCity.
-     * Used as string replacements when deploying 'labkey.xml' and 'application.properties'
-     */
-    @Input
-    Properties getExtraJdbcProperties()
-    {
-        def extraJdbcProperties = new Properties()
-        def tcProperties = isOnTeamCity.get() ? getTeamCityProperties(project) : new Properties()
-        for (Map.Entry entry : tcProperties.entrySet())
-        {
-            if (entry.getKey().startsWith("extraJdbc"))
-            {
-                extraJdbcProperties.put(entry.getKey(), entry.getValue())
-            }
-        }
-        return extraJdbcProperties
-    }
-
-    boolean embeddedConfigUpToDate()
-    {
-        if (this.dbPropertiesChanged)
-            return false
-
-        File dbPropFile = chosenPropsFile.get().getAsFile()
-        File _applicationPropsFile = applicationPropsFile.get().getAsFile()
-        if (!dbPropFile.exists() || !_applicationPropsFile.exists())
-            return false
-        if (dbPropFile.lastModified() < _applicationPropsFile.lastModified())
-        {
-            return true
-        }
-        return false
-    }
-
-    protected void setDatabaseProperties()
-    {
-        databaseProperties = new DatabaseProperties(getPath(), chosenPropsFile.get().asFile, false)
-    }
-
-    void setDatabaseProperties(DatabaseProperties dbProperties)
-    {
-        this.databaseProperties = dbProperties
+        setUpProperties()
     }
-
-    DatabaseProperties getDatabaseProperties()
-    {
-        return databaseProperties
-    }
-
-
-
-    void execSql(DatabaseProperties params, String sql)
-    {
-        params.interpolateCompositeProperties()
-        String url = params.getJdbcURL()
-        String user = params.getJdbcUser()
-        String password = params.getJdbcPassword()
-        String driverClassName = params.getJdbcDriverClassName()
-        logger.info("in execSql: url ${url} driverClassName ${driverClassName}")
-        logger.debug(" user ${user} password ${password}")
-
-        var loader = GroovyObject.class.classLoader
-        // N.B. It seems like this modification of the loader classpath should not be necessary (or possible) and we
-        // should be able to declare the dependencies on the driver jars in the buildscript { dependencies { } } block,
-        // but see this (admittedly old) post https://discuss.gradle.org/t/class-pathes-in-gradle-script/16655, which
-        // has a response that explains that "the caller to Sql isn't actually the build script, it is Groovy. So,
-        // you need to load the driver in the same classloader as Groovy." Maybe we'd have a different story if we
-        // were using Java instead of Groovy. Someday.
-        getDriverFiles().each {File file ->
-            logger.info("adding classLoader URL " + file.toURI().toURL())
-            loader.addURL(file.toURI().toURL())
-        }
-        Class driverClass = loader.loadClass(driverClassName)
-        logger.info("driverClass is ${driverClass}")
-
-        Driver driverInstance = (Driver) driverClass.newInstance()
-        DriverManager.registerDriver(driverInstance)
-
-        Sql db = null
-        try
-        {
-            db = Sql.newInstance(url, user, password)
-            db.execute(sql)
-        }
-        catch (Exception e)
-        {
-            logger.error(e.toString())
-        }
-        finally
-        {
-            if (db != null)
-                db.close()
-        }
-    }
-
-    void dropDatabase(String projectPath, DatabaseProperties dbProperties)
-    {
-        Properties properties = dbProperties.getConfigProperties()
-        logger.info("in dropDatabase for ${projectPath}, properties are ${properties}")
-        String toDrop = dbProperties.getJdbcDatabase()
-        if (toDrop == null || toDrop.equals("labkey"))
-        {
-            throw new GradleException("Must specify a database that is not 'labkey'")
-        }
-        else
-        {
-            DatabaseProperties dropProps = new DatabaseProperties(projectPath, dbProperties)
-            // need to connect to the built-in default database in order to drop the database
-            dropProps.setJdbcDatabase(dbProperties.getDefaultDatabase())
-            dropProps.setJdbcUrlParams("")
-
-            logger.info("Attempting to drop database ${toDrop}")
-            execSql(dropProps, "DROP DATABASE \"${toDrop}\";")
-        }
-    }
-
 }
diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
new file mode 100644
index 00000000..6733284d
--- /dev/null
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -0,0 +1,243 @@
+/*
+ * Copyright (c) 2016-2025 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.gradle.task
+
+import groovy.sql.Sql
+import org.gradle.api.GradleException
+import org.gradle.api.file.ConfigurableFileCollection
+import org.gradle.api.file.CopySpec
+import org.gradle.api.file.DuplicatesStrategy
+import org.gradle.api.file.FileSystemOperations
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.InputFile
+import org.gradle.api.tasks.InputFiles
+import org.gradle.api.tasks.Optional
+import org.gradle.api.tasks.OutputFile
+import org.labkey.gradle.util.BuildUtils
+import org.labkey.gradle.util.DatabaseProperties
+import org.labkey.gradle.util.PropertiesUtils
+
+import javax.inject.Inject
+import java.sql.Driver
+import java.sql.DriverManager
+
+abstract class SetUpProperties extends TeamCityPropertiesTask
+{
+    // TODO rethink this input declaration. Dependence on a file makes more sense
+    @Optional @Input
+    protected DatabaseProperties databaseProperties
+
+    @InputFiles
+    abstract ConfigurableFileCollection getDriverFiles()
+
+    @Input
+    boolean dbPropertiesChanged = false
+
+    @InputFile
+    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
+
+    @InputFile
+    final abstract RegularFileProperty applicationPropsFile = project.objects.fileProperty().fileValue(new File(BuildUtils.getEmbeddedConfigPath(project), "application.properties"))
+
+    @Input
+    final abstract Property<Boolean> useSsl = project.objects.property(Boolean).convention(project.hasProperty("useSsl"))
+    @Input
+    final abstract Property<String> portNumber = project.objects.property(String).convention(project.hasProperty("useSsl") ? "8443" : "8080")
+    @Input
+    final abstract Property<Boolean> useLocalBuild = project.objects.property(Boolean).convention(project.hasProperty("useLocalBuild") && "false" != project.property("useLocalBuild"))
+
+    @Input // in .properties files, backward slashes are seen as escape characters, so all paths must use forward slashes, even on Windows
+    final abstract Property<String> pathToServer = project.objects.property(String).convention(project.rootDir.getAbsolutePath().replaceAll("\\\\", "/"))
+
+    @Input
+    final abstract Property<String> embeddedDir = project.objects.property(String).convention(BuildUtils.getEmbeddedConfigPath(project))
+    @InputDirectory
+    File configsDir = new File(BuildUtils.getConfigsProject(project).projectDir, "configs")
+
+    @OutputFile
+    final abstract RegularFileProperty restartTriggerFile = project.objects.fileProperty().fileValue(BuildUtils.getRestartTriggerFile(project))
+
+    @Inject abstract FileSystemOperations getFs()
+
+    void setUpProperties() {
+        if (!embeddedConfigUpToDate()) {
+            Properties configProperties = databaseProperties.getConfigProperties()
+            configProperties.putAll(getExtraJdbcProperties())
+            configProperties.setProperty("pathToServer", pathToServer.get())
+            configProperties.setProperty("serverPort", labKeyServerPort.get())
+            configProperties.setProperty("contextPath", contextPath.get())
+            configProperties.setProperty("shutdownPort", shutdownPort.get())
+            if (useSsl.get()) {
+                configProperties.setProperty("keyStore", keyStore.get())
+                configProperties.setProperty("keyStorePassword", keyStorePassword.get())
+            }
+
+            fs.copy({ CopySpec copy ->
+                copy.from configsDir
+                copy.into embeddedDir.get()
+                copy.include "application.properties"
+                copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
+                copy.filter({ String line ->
+                    // Always uncomment properties prepended by '#setupTask#'
+                    line = line.replace("#setupTask#", "")
+                    if (useSsl.get()) {
+                        line = line.replace("#server.ssl", "server.ssl")
+                    }
+                    if (useLocalBuild.get()) {
+                        // Enable properties that require 'useLocalBuild' (e.g. 'context.webAppLocation' and 'spring.devtools.restart.additional-paths')
+                        line = line.replace("#useLocalBuild#", "")
+                    }
+                    else {
+                        // Remove placeholder
+                        line = line.replace("#useLocalBuild#", "#")
+                    }
+                    if (configProperties.containsKey("extraJdbcDataSource") && line.contains("=@@extraJdbc"))
+                    {
+                        line = line.replace("#context.", "context.")
+                    }
+                    if (configProperties.containsKey("contextPath") && line.contains("=@@contextPath"))
+                    {
+                        line = line.replace("#context.", "context.")
+                    }
+                    if (line.startsWith("#")) {
+                        return line // Don't apply replacements to comments
+                    }
+                    return PropertiesUtils.replaceProps(line, configProperties, false)
+                })
+            })
+            BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
+        }
+    }
+
+    /**
+     * Get 'extraJdbc*' properties from TeamCity.
+     * Used as string replacements when deploying 'labkey.xml' and 'application.properties'
+     */
+    @Input
+    Properties getExtraJdbcProperties()
+    {
+        def extraJdbcProperties = new Properties()
+        def tcProperties = isOnTeamCity.get() ? getTeamCityProperties(project) : new Properties()
+        for (Map.Entry entry : tcProperties.entrySet())
+        {
+            if (entry.getKey().startsWith("extraJdbc"))
+            {
+                extraJdbcProperties.put(entry.getKey(), entry.getValue())
+            }
+        }
+        return extraJdbcProperties
+    }
+
+    boolean embeddedConfigUpToDate()
+    {
+        if (this.dbPropertiesChanged)
+            return false
+
+        File dbPropFile = chosenPropsFile.get().getAsFile()
+        File _applicationPropsFile = applicationPropsFile.get().getAsFile()
+        if (!dbPropFile.exists() || !_applicationPropsFile.exists())
+            return false
+        if (dbPropFile.lastModified() < _applicationPropsFile.lastModified())
+        {
+            return true
+        }
+        return false
+    }
+
+    protected void setDatabaseProperties()
+    {
+        databaseProperties = new DatabaseProperties(getPath(), chosenPropsFile.get().asFile, false)
+    }
+
+    void setDatabaseProperties(DatabaseProperties dbProperties)
+    {
+        this.databaseProperties = dbProperties
+    }
+
+    DatabaseProperties getDatabaseProperties()
+    {
+        return databaseProperties
+    }
+
+    void execSql(DatabaseProperties params, String sql)
+    {
+        params.interpolateCompositeProperties()
+        String url = params.getJdbcURL()
+        String user = params.getJdbcUser()
+        String password = params.getJdbcPassword()
+        String driverClassName = params.getJdbcDriverClassName()
+        logger.info("in execSql: url ${url} driverClassName ${driverClassName}")
+        logger.debug(" user ${user} password ${password}")
+
+        var loader = GroovyObject.class.classLoader
+        // N.B. It seems like this modification of the loader classpath should not be necessary (or possible) and we
+        // should be able to declare the dependencies on the driver jars in the buildscript { dependencies { } } block,
+        // but see this (admittedly old) post https://discuss.gradle.org/t/class-pathes-in-gradle-script/16655, which
+        // has a response that explains that "the caller to Sql isn't actually the build script, it is Groovy. So,
+        // you need to load the driver in the same classloader as Groovy." Maybe we'd have a different story if we
+        // were using Java instead of Groovy. Someday.
+        getDriverFiles().each {File file ->
+            logger.info("adding classLoader URL " + file.toURI().toURL())
+            loader.addURL(file.toURI().toURL())
+        }
+        Class driverClass = loader.loadClass(driverClassName)
+        logger.info("driverClass is ${driverClass}")
+
+        Driver driverInstance = (Driver) driverClass.newInstance()
+        DriverManager.registerDriver(driverInstance)
+
+        Sql db = null
+        try
+        {
+            db = Sql.newInstance(url, user, password)
+            db.execute(sql)
+        }
+        catch (Exception e)
+        {
+            logger.error(e.toString())
+        }
+        finally
+        {
+            if (db != null)
+                db.close()
+        }
+    }
+
+    void dropDatabase(String projectPath, DatabaseProperties dbProperties)
+    {
+        Properties properties = dbProperties.getConfigProperties()
+        logger.info("in dropDatabase for ${projectPath}, properties are ${properties}")
+        String toDrop = dbProperties.getJdbcDatabase()
+        if (toDrop == null || toDrop.equals("labkey"))
+        {
+            throw new GradleException("Must specify a database that is not 'labkey'")
+        }
+        else
+        {
+            DatabaseProperties dropProps = new DatabaseProperties(projectPath, dbProperties)
+            // need to connect to the built-in default database in order to drop the database
+            dropProps.setJdbcDatabase(dbProperties.getDefaultDatabase())
+            dropProps.setJdbcUrlParams("")
+
+            logger.info("Attempting to drop database ${toDrop}")
+            execSql(dropProps, "DROP DATABASE \"${toDrop}\";")
+        }
+    }
+
+}

From b46317ffa010f57c45b00d723891b8efbb2926a2 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 09:20:53 -0700
Subject: [PATCH 33/61] restore nlp-related tasks temporarily since it's still
 configured in TC

---
 .../org/labkey/gradle/plugin/TeamCity.groovy  | 30 ++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 2467fd23..f16a3b8b 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -35,9 +35,11 @@ import org.gradle.api.UnknownTaskException
 import org.gradle.api.file.DeleteSpec
 import org.gradle.api.logging.Logger
 import org.gradle.api.provider.Provider
+import org.gradle.api.tasks.Copy
 import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.JavaExec
 import org.gradle.api.tasks.TaskProvider
+import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.PickDb
 import org.labkey.gradle.task.RunTestSuite
@@ -47,8 +49,10 @@ import org.labkey.gradle.task.UndeployModules
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.GroupNames
+import org.labkey.gradle.util.PropertiesUtils
 
 import java.time.Duration
+import java.util.regex.Matcher
 
 /**
  * Creates tasks for TeamCity to run its tests suites based on properties set in a build configuration (particularly for
@@ -57,7 +61,8 @@ import java.time.Duration
 class TeamCity extends Tomcat
 {
     private static final String TEAMCITY_INFO_FILE = "teamcity-info.xml"
-    private static final String TEST_CONFIGS_DIR = "configs/config-test"
+    private static final String TEST_CONFIGS_DIR = "configs/config-test" // TODO remove once NLP is not conifgured on TC
+    private static final String NLP_CONFIG_FILE = "nlpConfig.xml" // TODO remove once NLP is not configured on TC
     private static final String PIPELINE_CONFIG_FILE =  "pipelineConfig.xml"
     private static final Duration TOMCAT_SHUTDOWN_TIMEOUT = Duration.ofSeconds(15)
 
@@ -158,6 +163,29 @@ class TeamCity extends Tomcat
             dependsOn(project.tasks.createStartupPropertyFile)
         }
 
+        // TODO remove once no longer referenced in TeamCity
+        project.tasks.register("createNlpConfig", Copy) {
+            Copy task ->
+                task.group = GroupNames.TEST_SERVER
+                task.description = "Create NLP engine configs for the test server"
+                task.from BuildUtils.getServerProject(project).file(TEST_CONFIGS_DIR)
+                task.include NLP_CONFIG_FILE
+                task.inputs.property("directoryPath", new File((String) project.labkey.externalDir, "nlp/nlp_engine.py").getAbsolutePath())
+                task.filter({ String line ->
+                    Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
+                    String newLine = line
+                    while (matcher.find())
+                    {
+                        if (matcher.group(1).equals("enginePath"))
+                            newLine = newLine.replace(matcher.group(), (String) task.inputs.properties.get("directoryPath"))
+                    }
+                    return newLine
+                }
+                )
+                task.destinationDir = new File("${ServerDeployExtension.getServerDeployDirectoryPath(project)}/config")
+
+        }
+
         project.tasks.register("validateConfiguration") {
             Task task ->
                 task.doFirst

From a00aabfb5090ffd4c3e687d556b10545c503e928 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 16:18:33 -0700
Subject: [PATCH 34/61] Update distribution tasks for compatibility

---
 README.md                                     |  2 +
 .../gradle/task/DeployDistribution.groovy     | 19 ++++++---
 .../gradle/task/ModuleDistribution.groovy     | 39 +++++++++++++------
 .../gradle/task/StageDistribution.groovy      | 13 +++++--
 4 files changed, 53 insertions(+), 20 deletions(-)

diff --git a/README.md b/README.md
index 0cb077a4..d1daf68a 100644
--- a/README.md
+++ b/README.md
@@ -31,6 +31,8 @@ on how to do that, including how to develop and test locally and the versioning
 - Remove deprecated `getServerDeployDirectory` from `ServerDeployExtension`
 - TODO Remove `createNlpConfig` task from `TeamCity` plugin since that module is no longer in use
 - Remove `setup` task from `ServerDeploy` plugin.
+- Update `DeployDistribution` and `StageDistribution` for configuration cache compatibility
+- Some updates for `ModuleDistribution` for better configuration cache compatibility
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy b/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
index 1b0543a4..053f9030 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
@@ -1,15 +1,21 @@
 package org.labkey.gradle.task
 
+import org.gradle.api.file.ArchiveOperations
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
-import org.labkey.gradle.plugin.ServerDeploy
 import org.labkey.gradle.plugin.extension.DistributionExtension
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
 
-abstract class DeployDistribution extends DeployAppBase {
+import javax.inject.Inject
+
+abstract class DeployDistribution extends DeployAppBase
+{
+    @Inject abstract ArchiveOperations getArchiveOps()
 
     @OutputDirectory
     final abstract DirectoryProperty deployDir = project.objects.directoryProperty().convention(ServerDeployExtension.getEmbeddedDir(project))
@@ -17,24 +23,27 @@ abstract class DeployDistribution extends DeployAppBase {
     @OutputDirectory
     final abstract DirectoryProperty deployBinDir = project.objects.directoryProperty().convention(ServerDeployExtension.getEmbeddedBinDir(project))
 
+    @InputFile
+    final abstract RegularFileProperty distributionFile = project.objects.fileProperty().fileValue(DistributionExtension.getDistributionFile(project))
+
     @TaskAction
     void action()
     {
         deployExecutableJar()
         deployPlatformBinaries(deployBinDir.get().asFile)
+        setDatabaseProperties()
         setUpProperties()
     }
 
     private void deployExecutableJar() {
-        File distributionFile = DistributionExtension.getDistributionFile(project)
         fs.copy({ CopySpec copy ->
-            copy.from project.tarTree(distributionFile).files
+            copy.from archiveOps.tarTree(distributionFile.get().asFile).files
             copy.into deployDir.get()
             copy.include  "*.jar"
             copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
         })
         fs.copy({ CopySpec copy ->
-            copy.from project.tarTree(distributionFile).files
+            copy.from archiveOps.tarTree(distributionFile.get().asFile).files
             copy.into deployBinDir.get()
             copy.include   "*.exe", "*.dll"
             copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
diff --git a/src/main/groovy/org/labkey/gradle/task/ModuleDistribution.groovy b/src/main/groovy/org/labkey/gradle/task/ModuleDistribution.groovy
index c94aed25..ed6aa155 100644
--- a/src/main/groovy/org/labkey/gradle/task/ModuleDistribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/ModuleDistribution.groovy
@@ -21,15 +21,26 @@ import org.gradle.api.GradleException
 import org.gradle.api.Project
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DuplicatesStrategy
-import org.gradle.api.tasks.*
+import org.gradle.api.file.FileSystemOperations
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.Optional
+import org.gradle.api.tasks.OutputDirectory
+import org.gradle.api.tasks.OutputFile
+import org.gradle.api.tasks.OutputFiles
+import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.ApplyLicenses
 import org.labkey.gradle.plugin.extension.DistributionExtension
 import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 
-class ModuleDistribution extends DefaultTask
+import javax.inject.Inject
+
+abstract class ModuleDistribution extends DefaultTask
 {
+    @Inject abstract FileSystemOperations getFs()
+
     @Optional @Input
     String extraFileIdentifier = null
     @Optional @Input
@@ -45,6 +56,12 @@ class ModuleDistribution extends DefaultTask
     @Optional @Input
     Map extraProperties = [:]
 
+    @Input
+    final abstract Property<Boolean> isDevMode = project.objects.property(Boolean).convention(LabKeyExtension.isDevMode(project))
+
+    @Input
+    final abstract Property<Boolean> isDevDist = project.objects.property(Boolean).convention(project.hasProperty("devDistribution"))
+
     private File distributionDir
 
     private final DistributionExtension distExtension
@@ -90,7 +107,7 @@ class ModuleDistribution extends DefaultTask
     @TaskAction
     void doAction()
     {
-        if (LabKeyExtension.isDevMode(project) && !project.hasProperty("devDistribution"))
+        if (isDevMode.get() && !isDevDist.get())
             throw new GradleException("Distributions should never be created with deployMode=dev as dev modules are not portable. " +
                     "Use -PdevDistribution if you need to override this exception for debugging.")
 
@@ -126,7 +143,7 @@ class ModuleDistribution extends DefaultTask
     {
         File modulesDir = getModulesDir()
         modulesDir.deleteDir()
-        project.copy {
+        fs.copy {
             CopySpec copy ->
                 copy.from { project.configurations.distribution }
                 copy.setDuplicatesStrategy(DuplicatesStrategy.EXCLUDE)
@@ -134,7 +151,7 @@ class ModuleDistribution extends DefaultTask
         }
         if (!BuildUtils.isOpenSource(project))
         {
-            project.copy {
+            fs.copy {
                 CopySpec copy ->
                     copy.from(findLicensingProject().tasks.patchApiModule.outputs.files.singleFile)
                     copy.rename { String fileName ->
@@ -203,7 +220,7 @@ class ModuleDistribution extends DefaultTask
         File utilsDir = getWindowsUtilDir()
         if (project.configurations.findByName("utilities") != null && !utilsDir.exists())
         {
-            project.copy({
+            fs.copy({
                 CopySpec copy ->
                     copy.from(project.configurations.utilities.collect { project.zipTree(it) })
                     copy.into utilsDir
@@ -231,7 +248,7 @@ class ModuleDistribution extends DefaultTask
             }
         }
 
-        project.copy {
+        fs.copy {
             CopySpec copy ->
                 copy.from(embeddedJarFile)
                 copy.into(project.layout.buildDirectory)
@@ -276,7 +293,7 @@ class ModuleDistribution extends DefaultTask
         // Prefer files from 'server/configs/webapps' if they exist
         File serverConfigDir = project.rootProject.file("server/configs/webapps/")
         if (serverConfigDir.exists()) {
-            project.copy({ CopySpec copy ->
+            fs.copy({ CopySpec copy ->
                 copy.from(serverConfigDir)
                 copy.exclude "*.xml"
                 copy.into(project.layout.buildDirectory)
@@ -286,12 +303,12 @@ class ModuleDistribution extends DefaultTask
         // Allow distributions to include custom README
         File resources = project.file("resources")
         if (resources.isDirectory()) {
-            project.copy({ CopySpec copy ->
+            fs.copy({ CopySpec copy ->
                 copy.from(resources)
                 copy.into(project.layout.buildDirectory)
                 copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
             })
-            project.copy({ CopySpec copy ->
+            fs.copy({ CopySpec copy ->
                 copy.from(resources)
                 copy.into(project.layout.buildDirectory.file("embedded"))
                 copy.setDuplicatesStrategy(DuplicatesStrategy.INCLUDE)
@@ -300,7 +317,7 @@ class ModuleDistribution extends DefaultTask
         // This is necessary for reasons that are unclear. Without it, you get:
         // -bash: ./manual-upgrade.sh: /bin/sh^M: bad interpreter: No such file or directory
         // even though the original file has unix line endings. Dunno.
-        project.ant.fixcrlf (srcdir: BuildUtils.getBuildDirPath(project), includes: "manual-upgrade.sh", eol: "unix")
+        this.ant.fixcrlf (srcdir: BuildUtils.getBuildDirPath(project), includes: "manual-upgrade.sh", eol: "unix")
     }
 
     @OutputFile
diff --git a/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy b/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy
index 2e4247cd..4fe50ee1 100644
--- a/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy
@@ -16,13 +16,16 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.file.ArchiveOperations
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.file.FileCopyDetails
 import org.gradle.api.file.FileSystemOperations
 import org.gradle.api.file.FileTree
+import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.file.RelativePath
+import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.ServerDeploy
@@ -34,8 +37,7 @@ import javax.inject.Inject
 abstract class StageDistribution extends DefaultTask
 {
     @Inject abstract FileSystemOperations getFs()
-
-    protected File distributionFile = null
+    @Inject abstract ArchiveOperations getArchiveOps()
 
     @OutputDirectory
     final abstract DirectoryProperty modulesStagingDir = BuildUtils.getRootBuildDirectoryProperty(project, ServerDeploy.STAGING_MODULES_DIR)
@@ -46,12 +48,15 @@ abstract class StageDistribution extends DefaultTask
     @OutputDirectory
     final abstract DirectoryProperty pipelineJarStagingDir = BuildUtils.getRootBuildDirectoryProperty(project, ServerDeploy.STAGING_PIPELINE_DIR)
 
+    @InputFile
+    final abstract RegularFileProperty distributionFileProp = project.objects.fileProperty().fileValue(DistributionExtension.getDistributionFile(project))
+
     @TaskAction
     void action()
     {
-        distributionFile = DistributionExtension.getDistributionFile(project)
+        File distributionFile = distributionFileProp.get().asFile
         String extension = DistributionExtension.TAR_ARCHIVE_EXTENSION
-        FileTree distArchiveTree = project.tarTree(distributionFile)
+        FileTree distArchiveTree = archiveOps.tarTree(distributionFile)
 
         // first clean out the staging directory so we don't pick up modules not in this distribution
         fs.delete {

From 7df66281a98c8c3ee427d2c9722c9cdea146d791 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 16:18:48 -0700
Subject: [PATCH 35/61] Mark applicationProperties as output not input

---
 src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index 6733284d..e521fd5b 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -52,7 +52,7 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
     @InputFile
     final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
 
-    @InputFile
+    @OutputFile
     final abstract RegularFileProperty applicationPropsFile = project.objects.fileProperty().fileValue(new File(BuildUtils.getEmbeddedConfigPath(project), "application.properties"))
 
     @Input

From 2f8e241eb1cb4a4705c42984956cf16056dd74ed Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 18:58:07 -0700
Subject: [PATCH 36/61] space

---
 src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
index 25ac4009..7dec498c 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
@@ -30,7 +30,7 @@ abstract class TeamCityDbSetup extends DoThenSetup
     {
         databaseProperties.mergePropertiesFromFile()
         if (dropDatabase) {
-            if (testValidationOnly){
+            if (testValidationOnly) {
                 logger.info("The 'testValidationOnly' flag is true, not going to drop the database.")
             }
             else {

From 147c223c91eada8c4993a343c5e0a20e0188d5f3 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Thu, 14 Aug 2025 19:03:27 -0700
Subject: [PATCH 37/61] Another interation for DeployApp inputs and outputs

---
 src/main/groovy/org/labkey/gradle/task/DeployApp.groovy     | 1 +
 src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy | 6 ++++++
 .../groovy/org/labkey/gradle/task/SetUpProperties.groovy    | 6 +++---
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
index e3b9a88b..c6cd1dc9 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployApp.groovy
@@ -71,6 +71,7 @@ abstract class DeployApp extends DeployAppBase
         deployPipelineJars()
         deployPlatformBinaries(deployBinDir.get().asFile)
         deployEmbeddedBootJar()
+        setDatabaseProperties()
         setUpProperties()
         BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
     }
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy b/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
index 2f2d86d8..af5e0c1b 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
@@ -6,9 +6,12 @@ import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.file.FileSystemOperations
+import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.OutputDirectory
+import org.gradle.api.tasks.OutputFile
 import org.labkey.gradle.util.BuildUtils
+import org.labkey.gradle.util.DatabaseProperties
 
 import javax.inject.Inject
 
@@ -16,6 +19,9 @@ abstract class DeployAppBase extends SetUpProperties {
 
     @Inject abstract FileSystemOperations getFs()
 
+    @OutputFile
+    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
+
     @InputFiles
     abstract ConfigurableFileCollection getBinaries()
 
diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index e521fd5b..3e238d6e 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -27,6 +27,7 @@ import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputDirectory
 import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.InputFiles
+import org.gradle.api.tasks.Internal
 import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.OutputFile
 import org.labkey.gradle.util.BuildUtils
@@ -39,9 +40,8 @@ import java.sql.DriverManager
 
 abstract class SetUpProperties extends TeamCityPropertiesTask
 {
-    // TODO rethink this input declaration. Dependence on a file makes more sense
-    @Optional @Input
-    protected DatabaseProperties databaseProperties
+    @Internal
+    private DatabaseProperties databaseProperties
 
     @InputFiles
     abstract ConfigurableFileCollection getDriverFiles()

From 2710836d5959bebc59247abcc32d1fda52427f0c Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 06:24:57 -0700
Subject: [PATCH 38/61] Another iteration for chosenPropsFile input

---
 src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy     | 5 +++++
 src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy | 6 ------
 .../groovy/org/labkey/gradle/task/SetUpProperties.groovy    | 4 +---
 3 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy b/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
index 31c01006..6533a52e 100644
--- a/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
@@ -15,10 +15,15 @@
  */
 package org.labkey.gradle.task
 
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.tasks.InputFile
 import org.labkey.gradle.util.DatabaseProperties
 
 abstract class Bootstrap extends DoThenSetup
 {
+    @InputFile
+    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
+
     boolean dbPropertiesChanged = true
 
     @Override
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy b/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
index af5e0c1b..2f2d86d8 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployAppBase.groovy
@@ -6,12 +6,9 @@ import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.file.FileSystemOperations
-import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.OutputDirectory
-import org.gradle.api.tasks.OutputFile
 import org.labkey.gradle.util.BuildUtils
-import org.labkey.gradle.util.DatabaseProperties
 
 import javax.inject.Inject
 
@@ -19,9 +16,6 @@ abstract class DeployAppBase extends SetUpProperties {
 
     @Inject abstract FileSystemOperations getFs()
 
-    @OutputFile
-    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
-
     @InputFiles
     abstract ConfigurableFileCollection getBinaries()
 
diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index 3e238d6e..a5306e9e 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -25,10 +25,8 @@ import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputDirectory
-import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.Internal
-import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.OutputFile
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
@@ -49,7 +47,7 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
     @Input
     boolean dbPropertiesChanged = false
 
-    @InputFile
+    @OutputFile
     final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
 
     @OutputFile

From 900ce9a22fefa5c2a3a06ab465e6030c2aa67a25 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 09:01:20 -0700
Subject: [PATCH 39/61] Move methods for updating dbProps to TeamCityDbSetup
 task

---
 .../org/labkey/gradle/plugin/JsDoc.groovy     |  2 --
 .../org/labkey/gradle/task/DoThenSetup.groovy |  1 -
 .../labkey/gradle/task/TeamCityDbSetup.groovy | 19 ++++++++++++++-
 .../gradle/util/DatabaseProperties.groovy     | 23 +++----------------
 4 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy b/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
index 5f4fdaf0..4bad3a01 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/JsDoc.groovy
@@ -15,10 +15,8 @@
  */
 package org.labkey.gradle.plugin
 
-import org.gradle.api.DefaultTask
 import org.gradle.api.Plugin
 import org.gradle.api.Project
-import org.gradle.api.Task
 import org.gradle.api.file.DeleteSpec
 import org.gradle.api.tasks.Copy
 import org.gradle.api.tasks.Delete
diff --git a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
index 22889088..565069dc 100644
--- a/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DoThenSetup.groovy
@@ -15,7 +15,6 @@
  */
 package org.labkey.gradle.task
 
-
 import org.gradle.api.tasks.TaskAction
 
 abstract class DoThenSetup extends SetUpProperties
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
index 7dec498c..20d69e3f 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
@@ -16,6 +16,7 @@
 package org.labkey.gradle.task
 
 import org.gradle.api.tasks.Input
+import org.labkey.gradle.util.DatabaseProperties
 
 abstract class TeamCityDbSetup extends DoThenSetup
 {
@@ -38,7 +39,23 @@ abstract class TeamCityDbSetup extends DoThenSetup
             }
         }
         databaseProperties.interpolateCompositeProperties()
-        databaseProperties.writeDbProps()
+        writeDbProps()
     }
 
+    void writeDbProps()
+    {
+        writeDatabaseProperty(DatabaseProperties.JDBC_URL_PROP, databaseProperties.getJdbcURL())
+        writeDatabaseProperty(DatabaseProperties.JDBC_USER_PROP, databaseProperties.getJdbcUser())
+        writeDatabaseProperty(DatabaseProperties.JDBC_PASSWORD_PROP, databaseProperties.getJdbcPassword())
+    }
+
+    private void writeDatabaseProperty(String name, String value)
+    {
+        this.ant.propertyfile(
+                file: chosenPropsFile.get().asFile
+        )
+                {
+                    entry( key: name, value: value)
+                }
+    }
 }
diff --git a/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy b/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
index 03e37b82..9517f6d1 100644
--- a/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
@@ -25,13 +25,13 @@ class DatabaseProperties
     private static final String PICKED_DATABASE_CONFIG_FILE = "config.properties"
 
     private static final String JDBC_DRIVER_CLASS_NAME_PROP = "jdbcDriverClassName"
-    private static final String JDBC_URL_PROP = "jdbcURL"
+    public static final String JDBC_URL_PROP = "jdbcURL"
     private static final String JDBC_PORT_PROP = "jdbcPort"
     private static final String JDBC_DATABASE_PROP = "jdbcDatabase"
     private static final String JDBC_HOST_PROP = "jdbcHost"
     private static final String JDBC_URL_PARAMS_PROP = "jdbcURLParameters"
-    private static final String JDBC_USER_PROP = "jdbcUser"
-    private static final String JDBC_PASSWORD_PROP = "jdbcPassword"
+    public static final String JDBC_USER_PROP = "jdbcUser"
+    public static final String JDBC_PASSWORD_PROP = "jdbcPassword"
     private static final String BOOTSTRAP_DB_PROP = "databaseBootstrap"
     private static final String DEFAULT_DB_PROP = "databaseDefault"
     private static final String DEFAULT_HOST_PROP = "databaseDefaultHost"
@@ -224,13 +224,6 @@ class DatabaseProperties
         setDefaultJdbcProperties(false)
     }
 
-    void writeDbProps()
-    {
-        writeDatabaseProperty(_project, JDBC_URL_PROP, PropertiesUtils.parseCompositeProp(projectPath, this.configProperties, this.configProperties.getProperty(JDBC_URL_PROP), logger))
-        writeDatabaseProperty(_project, JDBC_USER_PROP, getJdbcUser())
-        writeDatabaseProperty(_project, JDBC_PASSWORD_PROP, getJdbcPassword())
-    }
-
     static Properties readDatabaseProperties(File configFile, Logger logger)
     {
         if (configFile.exists())
@@ -244,14 +237,4 @@ class DatabaseProperties
             return new Properties()
         }
     }
-
-    private void writeDatabaseProperty(Project project, String name, String value)
-    {
-        project.ant.propertyfile(
-                file: getPickedConfigFile(project)
-        )
-                {
-                    entry( key: name, value: value)
-                }
-    }
 }

From 65716888c610b042027ec651a9f3b0dbfbff5fa7 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 09:30:39 -0700
Subject: [PATCH 40/61] Pass in chosenPropsFile to remove project reference

---
 src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy      | 2 +-
 src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy | 2 +-
 .../groovy/org/labkey/gradle/util/DatabaseProperties.groovy   | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index f16a3b8b..921b81de 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -222,7 +222,7 @@ class TeamCity extends Tomcat
 
             String suffix = properties.dbTypeAndVersion.capitalize()
             String setUpTaskName = "setUp${suffix}"
-            project.tasks.register(setUpTaskName,TeamCityDbSetup) {
+            project.tasks.register(setUpTaskName, TeamCityDbSetup) {
                 TeamCityDbSetup task ->
                     task.group = GroupNames.TEST_SERVER
                     task.description = "Get database properties set up for running tests for ${suffix}"
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
index 20d69e3f..555e1328 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
@@ -29,7 +29,7 @@ abstract class TeamCityDbSetup extends DoThenSetup
     @Override
     protected void doDatabaseTask()
     {
-        databaseProperties.mergePropertiesFromFile()
+        databaseProperties.mergePropertiesFromFile(chosenPropsFile.get().asFile)
         if (dropDatabase) {
             if (testValidationOnly) {
                 logger.info("The 'testValidationOnly' flag is true, not going to drop the database.")
diff --git a/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy b/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
index 9517f6d1..f89025ff 100644
--- a/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/DatabaseProperties.groovy
@@ -198,9 +198,9 @@ class DatabaseProperties
         this.configProperties.setProperty(JDBC_URL_PROP, PropertiesUtils.parseCompositeProp(projectPath, this.configProperties, this.configProperties.getProperty(JDBC_URL_PROP), logger))
     }
 
-    void mergePropertiesFromFile()
+    void mergePropertiesFromFile(File chosenPropsFile)
     {
-        Properties fileProperties = readDatabaseProperties(BuildUtils.getConfigsProject(project).file(PICKED_DATABASE_CONFIG_FILE), logger)
+        Properties fileProperties = readDatabaseProperties(chosenPropsFile, logger)
         for (String name : fileProperties.propertyNames())
         {
             if (this.configProperties.getProperty(name) == null)

From 3a6e943755a3eb0a51e6aff28db62cc636d253ee Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:20:07 -0700
Subject: [PATCH 41/61] revise comment

---
 src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index a5306e9e..b98f0a59 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -188,8 +188,7 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
         // should be able to declare the dependencies on the driver jars in the buildscript { dependencies { } } block,
         // but see this (admittedly old) post https://discuss.gradle.org/t/class-pathes-in-gradle-script/16655, which
         // has a response that explains that "the caller to Sql isn't actually the build script, it is Groovy. So,
-        // you need to load the driver in the same classloader as Groovy." Maybe we'd have a different story if we
-        // were using Java instead of Groovy. Someday.
+        // you need to load the driver in the same classloader as Groovy."
         getDriverFiles().each {File file ->
             logger.info("adding classLoader URL " + file.toURI().toURL())
             loader.addURL(file.toURI().toURL())

From ed6be56aff9613c3b35e218012f88ee42f056158 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:20:19 -0700
Subject: [PATCH 42/61] Add TODO comment

---
 src/main/groovy/org/labkey/gradle/task/RestoreFromTrash.groovy | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/groovy/org/labkey/gradle/task/RestoreFromTrash.groovy b/src/main/groovy/org/labkey/gradle/task/RestoreFromTrash.groovy
index fa772b4f..9a14481b 100644
--- a/src/main/groovy/org/labkey/gradle/task/RestoreFromTrash.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/RestoreFromTrash.groovy
@@ -18,6 +18,8 @@ import org.labkey.gradle.util.BuildUtils
 
 import static org.labkey.gradle.task.PurgeArtifacts.Response
 
+// TODO for more flexibility and for configuration cache support, needs to be converted to read projects and versions
+// from a file, as for PurgeArtifacts
 class RestoreFromTrash extends DefaultTask
 {
     public static final String VERSION_PROPERTY = "restoreVersion"

From 631ab8bd88ead8f6f079ce59dbd30934519b536b Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:22:39 -0700
Subject: [PATCH 43/61] Convert project-related properties to inputs

---
 .../gradle/task/PurgeNpmAlphaVersions.groovy  | 27 +++++++++++++------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy b/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy
index 52143c9b..f5ddfe43 100644
--- a/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy
@@ -9,15 +9,18 @@ import org.apache.hc.client5.http.impl.classic.HttpClients
 import org.apache.hc.core5.http.HttpStatus
 import org.gradle.api.DefaultTask
 import org.gradle.api.GradleException
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.NpmRun
 
 import java.util.stream.Collectors
 
-class PurgeNpmAlphaVersions extends DefaultTask
+abstract class PurgeNpmAlphaVersions extends DefaultTask
 {
     private static final String REPOSITORY_NAME = 'libs-client-local'
     public static final String ALPHA_PREFIX_PROPERTY = 'alphaPrefix'
+    public static final String DRY_RUN_PROPERTY = 'dryRun'
     public static final String[] PACKAGE_NAMES = [
             '@labkey/api',
             '@labkey/assayreport',
@@ -29,13 +32,21 @@ class PurgeNpmAlphaVersions extends DefaultTask
             '@labkey/themes'
     ]
 
+    @Input
+    final abstract Property<String> alphaPrefixProp = project.objects.property(String).convention((String) project.property(ALPHA_PREFIX_PROPERTY))
+    @Input
+    final abstract Property<Boolean> isDryRun = project.objects.property(Boolean).convention(project.hasProperty(DRY_RUN_PROPERTY))
+    @Input
+    final abstract Property<String> artifactoryUrl = project.objects.property(String).convention((String) project.property('artifactory_contextUrl'))
+    @Input
+    final abstract Property<String> artifactoryUser = project.objects.property(String).convention((String) project.property('artifactory_user'))
+    @Input
+    final abstract Property<String> artifactoryPassword = project.objects.property(String).convention((String) project.property('artifactory_password'))
+
     @TaskAction
     void purgeVersions()
     {
-        String alphaPrefix
-        if (!project.hasProperty(ALPHA_PREFIX_PROPERTY))
-            throw new GradleException("No value provided for alphaPrefix.")
-        alphaPrefix = project.property(ALPHA_PREFIX_PROPERTY)
+        String alphaPrefix = alphaPrefixProp.get()
         String[] undeletedVersions = []
         for (String packageName : PACKAGE_NAMES)
         {
@@ -47,7 +58,7 @@ class PurgeNpmAlphaVersions extends DefaultTask
                 logger.quiet("Found ${alphaVersions.size()} versions with alpha prefix ${alphaPrefix} in package ${packageName}")
                 if (!alphaVersions.isEmpty()) {
                     alphaVersions.forEach(version -> {
-                        if (project.hasProperty("dryRun"))
+                        if (isDryRun.get())
                             logger.quiet("Removing version ${version} of package ${packageName} -- Skipped for dry run")
                         else {
                             logger.quiet("Removing version ${version} of package ${packageName}")
@@ -109,7 +120,7 @@ class PurgeNpmAlphaVersions extends DefaultTask
     boolean makeDeleteRequest(String packageName, String version)
     {
         CloseableHttpClient httpClient = HttpClients.createDefault()
-        String endpoint = project.property('artifactory_contextUrl')
+        String endpoint = artifactoryUrl.get()
         boolean success = true
         if (!endpoint.endsWith("/"))
             endpoint += "/"
@@ -121,7 +132,7 @@ class PurgeNpmAlphaVersions extends DefaultTask
         {
             HttpDelete httpDelete = new HttpDelete(endpoint)
             // N.B. Using Authorization Bearer with an API token does not currently work
-            httpDelete.setHeader("Authorization", "Basic " + Base64.getEncoder().encodeToString("${project.property('artifactory_user')}:${project.property('artifactory_password')}".getBytes()))
+            httpDelete.setHeader("Authorization", "Basic " + Base64.getEncoder().encodeToString("${artifactoryUser.get()}:${artifactoryPassword.get()}".getBytes()))
             CloseableHttpResponse response = httpClient.execute(httpDelete)
             int statusCode = response.getCode()
             if (statusCode != HttpStatus.SC_OK && statusCode != HttpStatus.SC_NO_CONTENT) {

From d0bd0f678737d56d3a6cafb7bf466cd6bd1a9a25 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:22:54 -0700
Subject: [PATCH 44/61] Add incompatibility notes

---
 src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy | 1 +
 src/main/groovy/org/labkey/gradle/plugin/UiTest.groovy       | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index 2e502db9..0ec645d8 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -238,6 +238,7 @@ class ServerDeploy implements Plugin<Project>
             UndeployModules task ->
                 task.group = GroupNames.DEPLOY
                 task.description = "Removes all module files and directories from the deploy and staging directories"
+                task.notCompatibleWithConfigurationCache("Walks the project tree")
         }
 
         project.tasks.register(
diff --git a/src/main/groovy/org/labkey/gradle/plugin/UiTest.groovy b/src/main/groovy/org/labkey/gradle/plugin/UiTest.groovy
index 1ce12a0f..1e3e247c 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/UiTest.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/UiTest.groovy
@@ -93,6 +93,7 @@ class UiTest implements Plugin<Project>
                     task.mustRunAfter(serverProject.tasks.pickPg)
                     task.mustRunAfter(serverProject.tasks.pickMSSQL)
                 }
+                task.notCompatibleWithConfigurationCache("Needs some properties set for various project references.")
         }
     }
 

From 49012a6b24815756377eae3d1019c4442114db89 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:23:28 -0700
Subject: [PATCH 45/61] Set driver files and add missing dependencies for
 startTomcat

---
 .../groovy/org/labkey/gradle/plugin/TeamCity.groovy    | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 921b81de..127e7c65 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -228,6 +228,7 @@ class TeamCity extends Tomcat
                     task.description = "Get database properties set up for running tests for ${suffix}"
                     task.setDatabaseProperties(properties)
                     task.dropDatabase = extension.dropDatabase
+                    task.driverFiles.setFrom(project.configurations.driver)
                     task.testValidationOnly = Boolean.parseBoolean( extension.getTeamCityProperty("testValidationOnly"))
                     task.dependsOn (pickDbTask)
             }
@@ -250,14 +251,20 @@ class TeamCity extends Tomcat
                         task.dbType = properties.shortType
                         task.mustRunAfter(BuildUtils.getServerProject(project).tasks.pickMSSQL)
                         task.mustRunAfter(BuildUtils.getServerProject(project).tasks.pickPg)
+                        task.notCompatibleWithConfigurationCache("Walks the project tree")
                 }
             }
             undeployTask = project.tasks.named(undeployTaskName)
             project.tasks.named("startLabKey").configure {
-                mustRunAfter(undeployTask)
+                it.mustRunAfter(undeployTask)
+            }
+
+            project.tasks.named("startTomcat").configure {
+                it.mustRunAfter(undeployTask)
             }
 
             project.project(BuildUtils.getTestProjectPath(project.gradle)).tasks.startLabKey.mustRunAfter(setUpDbTask)
+            project.project(BuildUtils.getTestProjectPath(project.gradle)).tasks.startTomcat.mustRunAfter(setUpDbTask)
             String ciTestTaskName = "ciTests" + properties.dbTypeAndVersion.capitalize()
             project.tasks.register(ciTestTaskName, RunTestSuite) {
                 RunTestSuite task ->
@@ -268,6 +275,7 @@ class TeamCity extends Tomcat
                     task.mustRunAfter(project.tasks.validateConfiguration)
                     task.mustRunAfter(project.tasks.cleanTestLogs)
                     task.mustRunAfter(project.tasks.startLabKey)
+                    task.mustRunAfter(project.tasks.startTomcat)
             }
 
             ciTests.add(project.tasks.named(ciTestTaskName))

From aa61d1ee380f90ecd656ff6b22eb9a03f145100d Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:57:57 -0700
Subject: [PATCH 46/61] Remove incompatibility note

---
 src/main/groovy/org/labkey/gradle/plugin/JavaModule.groovy | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/JavaModule.groovy b/src/main/groovy/org/labkey/gradle/plugin/JavaModule.groovy
index 0e6fe16d..8940537a 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/JavaModule.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/JavaModule.groovy
@@ -157,10 +157,6 @@ class JavaModule implements Plugin<Project>
                     })
         }
 
-        project.tasks.named('populateExplodedLib') {
-            notCompatibleWithConfigurationCache("Need to figure out how to make the inputs from the optional tasks work.")
-        }
-
         project.tasks.named('module').configure {dependsOn(populateLib)}
         // We do this afterEvaluate to allow all dependencies to be declared before checking
         project.afterEvaluate({

From c595ff5b04d2cfad30c31f6d627ca083bc57f73f Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Fri, 15 Aug 2025 10:58:48 -0700
Subject: [PATCH 47/61] Convert `stageRemovePipelineJobs` and add back another
 stopTomcat dependency

---
 .../labkey/gradle/plugin/ServerDeploy.groovy  | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
index 0ec645d8..0edd0813 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy
@@ -128,26 +128,23 @@ class ServerDeploy implements Plugin<Project>
             Task task ->
                 task.group = GroupNames.DEPLOY
                 task.description = "Copy files needed for using remote pipeline jobs into ${stagingPipelineLibDir}"
+                task.inputs.files(project.configurations.remotePipelineJars.getFiles())
+                task.outputs.dir(BuildUtils.getRootBuildDirFile(project, STAGING_PIPELINE_DIR))
                 task.doLast({
-                    if (!project.configurations.remotePipelineJars.getFiles().isEmpty()) {
-                        task.ant.copy(
-                            todir: stagingPipelineLibDir,
+                    if (!inputs.files.isEmpty()) {
+                        ant.copy(
+                            todir: outputs.files.singleFile,
                             preserveLastModified: true
                         )
                         {
-                            project.configurations.remotePipelineJars
-                            {
-                                Configuration collection ->
-                                    collection.addToAntBuilder(project.ant, "fileset", FileCollection.AntType.FileSet)
-                            }
+                            inputs.files.addToAntBuilder(ant, "fileset", FileCollection.AntType.FileSet)
                         }
                     }
                 })
         }
 
         project.tasks.named('stageRemotePipelineJars').configure {
-            dependsOn project.configurations.remotePipelineJars
-            notCompatibleWithConfigurationCache("TODO Needs dedicated task class with configuration as input")
+            it.dependsOn project.configurations.remotePipelineJars
         }
 
         project.tasks.register(
@@ -275,9 +272,11 @@ class ServerDeploy implements Plugin<Project>
 
         project.tasks.named("cleanBuild").configure {
             it.dependsOn(project.tasks.stopLabKey)
+            it.mustRunAfter(project.tasks.stopTomcat)
         }
         project.tasks.named("cleanDeploy").configure {
             it.dependsOn(project.tasks.stopLabKey)
+            it.mustRunAfter(project.tasks.stopTomcat)
         }
     }
 

From 10277762120072e9c5677bc9975453fcd55ebb38 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 18 Aug 2025 08:02:43 -0700
Subject: [PATCH 48/61] Update `ProeprtiesUtils` to remove code for supporting
 `labkey.xml`

---
 README.md                                        |  1 +
 .../labkey/gradle/task/SetUpProperties.groovy    |  4 ++--
 .../labkey/gradle/util/PropertiesUtils.groovy    | 16 +++-------------
 3 files changed, 6 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index d1daf68a..f2d8a815 100644
--- a/README.md
+++ b/README.md
@@ -33,6 +33,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Remove `setup` task from `ServerDeploy` plugin.
 - Update `DeployDistribution` and `StageDistribution` for configuration cache compatibility
 - Some updates for `ModuleDistribution` for better configuration cache compatibility
+- Update `ProeprtiesUtils` to remove code for supporting `labkey.xml`
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index b98f0a59..72b887a4 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -116,7 +116,7 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
                     if (line.startsWith("#")) {
                         return line // Don't apply replacements to comments
                     }
-                    return PropertiesUtils.replaceProps(line, configProperties, false)
+                    return PropertiesUtils.replaceProps(line, configProperties)
                 })
             })
             BuildUtils.updateRestartTriggerFile(useLocalBuild.get(), restartTriggerFile.get().asFile)
@@ -125,7 +125,7 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
 
     /**
      * Get 'extraJdbc*' properties from TeamCity.
-     * Used as string replacements when deploying 'labkey.xml' and 'application.properties'
+     * Used as string replacements when deploying 'application.properties'
      */
     @Input
     Properties getExtraJdbcProperties()
diff --git a/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy b/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy
index d1104ea4..b7a4dc78 100644
--- a/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/PropertiesUtils.groovy
@@ -15,7 +15,6 @@
  */
 package org.labkey.gradle.util
 
-import org.apache.commons.text.StringEscapeUtils
 import org.gradle.api.Project
 import org.slf4j.Logger
 
@@ -67,33 +66,24 @@ class PropertiesUtils
         return prop
     }
 
-    static String replacePropInLine(String line, String propName, Object val, Boolean xmlEncode)
+    static String replacePropInLine(String line, String propName, Object val)
     {
         if (val != null)
         {
             String stringVal = val.toString()
-            if (xmlEncode)
-                stringVal = StringEscapeUtils.escapeXml10(stringVal)
             return line.replace("@@" + propName + "@@", stringVal)
         }
         return line
     }
 
-    static String replaceProps(String line, Properties props, Boolean xmlEncode = false)
+    static String replaceProps(String line, Properties props)
     {
         Matcher matcher = PROPERTY_PATTERN.matcher(line)
         while (matcher.find())
         {
             String propName = matcher.group(1)
             if (props.containsKey(propName))
-                line = replacePropInLine(line, propName, props.get(propName), xmlEncode)
-            // backward compatibility for labkey.xml having new prop name and config.properties having old one
-            // TODO remove these cases once we move to a plugin version that doesn't need to support backward compatibility
-            else if (propName.equals(ENCRYPTION_KEY_PROP_NAME) && props.containsKey(DEPRECATED_ENCRYPTION_KEY_PROP_NAME))
-                line = replacePropInLine(line, propName, props.get(DEPRECATED_ENCRYPTION_KEY_PROP_NAME), xmlEncode)
-            // backward compatibility for labkey.xml having old prop name and config.properties having new one
-            else if (propName.equals(DEPRECATED_ENCRYPTION_KEY_PROP_NAME) && props.containsKey(ENCRYPTION_KEY_PROP_NAME))
-                line = replacePropInLine(line, propName, props.get(ENCRYPTION_KEY_PROP_NAME), xmlEncode)
+                line = replacePropInLine(line, propName, props.get(propName))
         }
         return line
     }

From f736a0f4d32b6312c46d455dcd0337df33dfde18 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 19 Aug 2025 06:14:30 -0700
Subject: [PATCH 49/61] typo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f2d8a815..192f56f3 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Remove `setup` task from `ServerDeploy` plugin.
 - Update `DeployDistribution` and `StageDistribution` for configuration cache compatibility
 - Some updates for `ModuleDistribution` for better configuration cache compatibility
-- Update `ProeprtiesUtils` to remove code for supporting `labkey.xml`
+- Update `PropertiesUtils` to remove code for supporting `labkey.xml`
 
 ### 6.3.0
 *Released*: 3 July 2025

From 6189944dca25c7c539c40b5f8728c44884334606 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 15 Sep 2025 16:07:33 -0700
Subject: [PATCH 50/61] Move restart trigger out of `modules` directory so it
 doesn't cause that directory to be created when not otherwise used (e.g., for
 TeamCity's distribution deployment

---
 src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
index 5abeed3a..91d5f57b 100644
--- a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
@@ -895,7 +895,7 @@ class BuildUtils
 
     static File getRestartTriggerFile(Project project)
     {
-        return project.rootProject.layout.buildDirectory.file("deploy/modules/" + RESTART_FILE_NAME).get().getAsFile()
+        return project.rootProject.layout.buildDirectory.file("deploy/" + RESTART_FILE_NAME).get().getAsFile()
     }
 
     static void updateRestartTriggerFile(boolean useLocalBuild, File triggerFile)

From c6271e1f2581dd4a297b3fabed1562192743cf29 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 15 Sep 2025 16:49:38 -0700
Subject: [PATCH 51/61] Allow for no alphaPrefix during configuration

---
 .../org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy       | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy b/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy
index f5ddfe43..c73db094 100644
--- a/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/PurgeNpmAlphaVersions.groovy
@@ -33,7 +33,7 @@ abstract class PurgeNpmAlphaVersions extends DefaultTask
     ]
 
     @Input
-    final abstract Property<String> alphaPrefixProp = project.objects.property(String).convention((String) project.property(ALPHA_PREFIX_PROPERTY))
+    final abstract Property<String> alphaPrefixProp = project.objects.property(String).convention((project.hasProperty(ALPHA_PREFIX_PROPERTY) ? (String) project.property(ALPHA_PREFIX_PROPERTY) : null))
     @Input
     final abstract Property<Boolean> isDryRun = project.objects.property(Boolean).convention(project.hasProperty(DRY_RUN_PROPERTY))
     @Input
@@ -46,6 +46,8 @@ abstract class PurgeNpmAlphaVersions extends DefaultTask
     @TaskAction
     void purgeVersions()
     {
+        if (!alphaPrefixProp.isPresent() || StringUtils.isEmpty(alphaPrefixProp.get().trim()))
+            throw new GradleException("No value provided for alphaPrefix.")
         String alphaPrefix = alphaPrefixProp.get()
         String[] undeletedVersions = []
         for (String packageName : PACKAGE_NAMES)

From ab6b654499049bfb03e0a6f6a5f917c86aa826c1 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 15 Sep 2025 16:50:56 -0700
Subject: [PATCH 52/61] Allow for better error messaging for missing
 distributionFileProp

---
 .../extension/DistributionExtension.groovy    | 42 +++++++++----------
 .../gradle/task/DeployDistribution.groovy     | 14 ++++++-
 .../gradle/task/StageDistribution.groovy      |  7 +++-
 3 files changed, 38 insertions(+), 25 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
index 02a2c206..77fd1f27 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
@@ -15,7 +15,7 @@
  */
 package org.labkey.gradle.plugin.extension
 
-import org.gradle.api.GradleException
+
 import org.gradle.api.Project
 
 import java.nio.file.Paths
@@ -37,27 +37,25 @@ class DistributionExtension
         this.project = project
     }
 
-    static File getDistributionFile(Project project) {
-        File distDir = new File(project.rootDir, "dist")
-        if (project.hasProperty("distDir"))
-        {
-            if (Paths.get((String) project.property('distDir')).isAbsolute())
-                distDir = new File((String) project.property('distDir'))
-            else
-                distDir = new File(project.rootDir, (String) project.property("distDir"))
+    static File getDistributionFile(Project project, String distDirName) {
+        File distDir
+        if (Paths.get(distDirName).isAbsolute())
+            distDir = new File((String) project.property('distDir'))
+        else
+            distDir = new File(project.rootDir, distDirName)
+        if (distDir.exists()) {
+            File[] distFiles = distDir.listFiles(new FilenameFilter() {
+                @Override
+                boolean accept(File dir, String name)
+                {
+                    return name.endsWith(TAR_ARCHIVE_EXTENSION)
+                }
+            })
+            if (distFiles == null || distFiles.length == 0 || distFiles.length > 1)
+                return null
+
+            return distFiles[0]
         }
-        if (!distDir.exists())
-            throw new GradleException("Distribution directory ${distDir} not found")
-        File[] distFiles = distDir.listFiles(new FilenameFilter() {
-            @Override
-            boolean accept(File dir, String name) {
-                return name.endsWith(TAR_ARCHIVE_EXTENSION)
-            }
-        })
-        if (distFiles == null || distFiles.length == 0)
-            throw new GradleException("No distribution found in directory ${distDir} with extension ${TAR_ARCHIVE_EXTENSION}")
-        else if (distFiles.length > 1)
-            throw new GradleException("${distDir} contains ${distFiles.length} files with extension ${TAR_ARCHIVE_EXTENSION}. Only one is allowed.")
-        return distFiles[0]
+        return null
     }
 }
diff --git a/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy b/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
index 053f9030..216a0ce1 100644
--- a/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/DeployDistribution.groovy
@@ -1,11 +1,15 @@
 package org.labkey.gradle.task
 
+import org.gradle.api.GradleException
 import org.gradle.api.file.ArchiveOperations
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFile
+import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.extension.DistributionExtension
@@ -17,18 +21,24 @@ abstract class DeployDistribution extends DeployAppBase
 {
     @Inject abstract ArchiveOperations getArchiveOps()
 
+    @Input
+    final abstract Property<String> distDir = project.objects.property(String).convention(project.hasProperty("distDir") ? (String) project.property("distDir") : "dist")
+
     @OutputDirectory
     final abstract DirectoryProperty deployDir = project.objects.directoryProperty().convention(ServerDeployExtension.getEmbeddedDir(project))
 
     @OutputDirectory
     final abstract DirectoryProperty deployBinDir = project.objects.directoryProperty().convention(ServerDeployExtension.getEmbeddedBinDir(project))
 
-    @InputFile
-    final abstract RegularFileProperty distributionFile = project.objects.fileProperty().fileValue(DistributionExtension.getDistributionFile(project))
+    @InputFile @Optional
+    final abstract RegularFileProperty distributionFile = project.objects.fileProperty().fileValue(DistributionExtension.getDistributionFile(project, distDir.get()))
 
     @TaskAction
     void action()
     {
+        if (!distributionFile.isPresent())
+            throw new GradleException("Distribution file not found in directory '${distDir.get()}'. Be sure the directory exists and contains exactly one file with extension ${DistributionExtension.TAR_ARCHIVE_EXTENSION}.")
+
         deployExecutableJar()
         deployPlatformBinaries(deployBinDir.get().asFile)
         setDatabaseProperties()
diff --git a/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy b/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy
index 4fe50ee1..13362e6f 100644
--- a/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StageDistribution.groovy
@@ -25,6 +25,8 @@ import org.gradle.api.file.FileSystemOperations
 import org.gradle.api.file.FileTree
 import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.file.RelativePath
+import org.gradle.api.provider.Property
+import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFile
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
@@ -39,6 +41,9 @@ abstract class StageDistribution extends DefaultTask
     @Inject abstract FileSystemOperations getFs()
     @Inject abstract ArchiveOperations getArchiveOps()
 
+    @Input
+    final abstract Property<String> distDir = project.objects.property(String).convention(project.hasProperty("distDir") ? (String) project.property("distDir") : "dist")
+
     @OutputDirectory
     final abstract DirectoryProperty modulesStagingDir = BuildUtils.getRootBuildDirectoryProperty(project, ServerDeploy.STAGING_MODULES_DIR)
 
@@ -49,7 +54,7 @@ abstract class StageDistribution extends DefaultTask
     final abstract DirectoryProperty pipelineJarStagingDir = BuildUtils.getRootBuildDirectoryProperty(project, ServerDeploy.STAGING_PIPELINE_DIR)
 
     @InputFile
-    final abstract RegularFileProperty distributionFileProp = project.objects.fileProperty().fileValue(DistributionExtension.getDistributionFile(project))
+    final abstract RegularFileProperty distributionFileProp = project.objects.fileProperty().fileValue(DistributionExtension.getDistributionFile(project, distDir.get()))
 
     @TaskAction
     void action()

From 62091c840f47ee8eedbb4aa0e70145f1ded2990a Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 15 Sep 2025 17:05:07 -0700
Subject: [PATCH 53/61] Update comment

---
 src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
index 91d5f57b..43e80d40 100644
--- a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
@@ -879,11 +879,11 @@ class BuildUtils
     }
 
     /**
-     * Writes a file in the build/deploy/modules directory that can be used as a trigger file for restarting
+     * Writes a file in the build/deploy directory that can be used as a trigger file for restarting
      * SpringBoot. Without this, restarts may happen before the full application deployment is done, resulting
      * in a failed start. See
      * https://docs.spring.io/spring-boot/docs/current/reference/htmlsingle/#using.devtools.restart.triggerfile
-     * We use build/deploy/modules because when using a local build it's added in the application.properties file as a
+     * We use build/deploy because when using a local build it's added in the application.properties file as a
      * spring.devtools.restart.additional-paths
      *
      * @param project - for use in getting the rootProject's build directory

From 48d4e7ec55a4f3d2435b17a21c9d23fa6537e802 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 16 Sep 2025 14:31:07 -0700
Subject: [PATCH 54/61] Fix up bootstrap task so it will always run and will
 update the application.properties file and fix up executeSql method so it
 finds the right drivers

---
 README.md                                     |  2 ++
 .../org/labkey/gradle/plugin/Database.groovy  |  2 ++
 .../org/labkey/gradle/plugin/TeamCity.groovy  |  1 +
 .../org/labkey/gradle/task/Bootstrap.groovy   |  7 ------
 .../labkey/gradle/task/SetUpProperties.groovy | 25 ++++++-------------
 .../labkey/gradle/task/TeamCityDbSetup.groovy |  1 -
 6 files changed, 12 insertions(+), 26 deletions(-)

diff --git a/README.md b/README.md
index 192f56f3..a34693ed 100644
--- a/README.md
+++ b/README.md
@@ -34,6 +34,8 @@ on how to do that, including how to develop and test locally and the versioning
 - Update `DeployDistribution` and `StageDistribution` for configuration cache compatibility
 - Some updates for `ModuleDistribution` for better configuration cache compatibility
 - Update `PropertiesUtils` to remove code for supporting `labkey.xml`
+- Relocate the `.restartTriggerFile` to prevent creation of empty `build/deploy/modules` directory for embedded distribution deployment
+- Fix `bootstrap` task so it will update `application.properties`
 
 ### 6.3.0
 *Released*: 3 July 2025
diff --git a/src/main/groovy/org/labkey/gradle/plugin/Database.groovy b/src/main/groovy/org/labkey/gradle/plugin/Database.groovy
index 47eb377e..cbbc0f1f 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Database.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Database.groovy
@@ -74,6 +74,8 @@ class Database implements Plugin<Project>
                 task.group = GroupNames.DATABASE
                 task.description = "Switch to bootstrap database properties as defined in current db.config file"
                 task.driverFiles.setFrom(project.configurations.driver)
+                task.dbPropertiesChanged = true
+                task.outputs.upToDateWhen({ return false })
         }
     }
 }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 127e7c65..bf38d26e 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -228,6 +228,7 @@ class TeamCity extends Tomcat
                     task.description = "Get database properties set up for running tests for ${suffix}"
                     task.setDatabaseProperties(properties)
                     task.dropDatabase = extension.dropDatabase
+                    task.dbPropertiesChanged = true
                     task.driverFiles.setFrom(project.configurations.driver)
                     task.testValidationOnly = Boolean.parseBoolean( extension.getTeamCityProperty("testValidationOnly"))
                     task.dependsOn (pickDbTask)
diff --git a/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy b/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
index 6533a52e..572e1173 100644
--- a/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/Bootstrap.groovy
@@ -15,17 +15,10 @@
  */
 package org.labkey.gradle.task
 
-import org.gradle.api.file.RegularFileProperty
-import org.gradle.api.tasks.InputFile
 import org.labkey.gradle.util.DatabaseProperties
 
 abstract class Bootstrap extends DoThenSetup
 {
-    @InputFile
-    final abstract RegularFileProperty chosenPropsFile =  project.objects.fileProperty().fileValue(DatabaseProperties.getPickedConfigFile(project))
-
-    boolean dbPropertiesChanged = true
-
     @Override
     protected void doDatabaseTask()
     {
diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index 72b887a4..6d3b162a 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -183,37 +183,26 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
         logger.info("in execSql: url ${url} driverClassName ${driverClassName}")
         logger.debug(" user ${user} password ${password}")
 
-        var loader = GroovyObject.class.classLoader
+        var sqlLoader = Sql.classLoader
         // N.B. It seems like this modification of the loader classpath should not be necessary (or possible) and we
         // should be able to declare the dependencies on the driver jars in the buildscript { dependencies { } } block,
-        // but see this (admittedly old) post https://discuss.gradle.org/t/class-pathes-in-gradle-script/16655, which
-        // has a response that explains that "the caller to Sql isn't actually the build script, it is Groovy. So,
-        // you need to load the driver in the same classloader as Groovy."
+        // but see this (admittedly old) post about how the classloader is behaving and the suggested solution (pre Gradle 9, but still)
+        // https://stackoverflow.com/questions/44740416/drivermanager-doesnt-see-dependency-in-gradle-custom-plugins-task
         getDriverFiles().each {File file ->
             logger.info("adding classLoader URL " + file.toURI().toURL())
-            loader.addURL(file.toURI().toURL())
+            sqlLoader.addURL(file.toURI().toURL())
         }
-        Class driverClass = loader.loadClass(driverClassName)
-        logger.info("driverClass is ${driverClass}")
 
-        Driver driverInstance = (Driver) driverClass.newInstance()
-        DriverManager.registerDriver(driverInstance)
-
-        Sql db = null
         try
         {
-            db = Sql.newInstance(url, user, password)
-            db.execute(sql)
+            Sql.withInstance(url, user, password, driverClassName) {
+                it.execute sql
+            }
         }
         catch (Exception e)
         {
             logger.error(e.toString())
         }
-        finally
-        {
-            if (db != null)
-                db.close()
-        }
     }
 
     void dropDatabase(String projectPath, DatabaseProperties dbProperties)
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
index 555e1328..88f2d300 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityDbSetup.groovy
@@ -20,7 +20,6 @@ import org.labkey.gradle.util.DatabaseProperties
 
 abstract class TeamCityDbSetup extends DoThenSetup
 {
-    boolean dbPropertiesChanged = true
     @Input
     boolean dropDatabase = false
     @Input

From 393fd741b27c4755155975c98dc830c823a7568a Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Tue, 16 Sep 2025 14:32:11 -0700
Subject: [PATCH 55/61] Remove `createNlpConfig`

---
 README.md                                     |  2 +-
 .../org/labkey/gradle/plugin/TeamCity.groovy  | 23 -------------------
 2 files changed, 1 insertion(+), 24 deletions(-)

diff --git a/README.md b/README.md
index a34693ed..21da78dc 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ on how to do that, including how to develop and test locally and the versioning
 - Update `GzipAction` task to use task logger and ant builder objects
 - Update `StopLabKey` and `StartLabKey` with appropriate dependencies to mirror the deprecated `StopTomcat` and `StartTomcat`
 - Remove deprecated `getServerDeployDirectory` from `ServerDeployExtension`
-- TODO Remove `createNlpConfig` task from `TeamCity` plugin since that module is no longer in use
+- Remove `createNlpConfig` task from `TeamCity` plugin since that module is no longer in use
 - Remove `setup` task from `ServerDeploy` plugin.
 - Update `DeployDistribution` and `StageDistribution` for configuration cache compatibility
 - Some updates for `ModuleDistribution` for better configuration cache compatibility
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index bf38d26e..21bb1f86 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -163,29 +163,6 @@ class TeamCity extends Tomcat
             dependsOn(project.tasks.createStartupPropertyFile)
         }
 
-        // TODO remove once no longer referenced in TeamCity
-        project.tasks.register("createNlpConfig", Copy) {
-            Copy task ->
-                task.group = GroupNames.TEST_SERVER
-                task.description = "Create NLP engine configs for the test server"
-                task.from BuildUtils.getServerProject(project).file(TEST_CONFIGS_DIR)
-                task.include NLP_CONFIG_FILE
-                task.inputs.property("directoryPath", new File((String) project.labkey.externalDir, "nlp/nlp_engine.py").getAbsolutePath())
-                task.filter({ String line ->
-                    Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
-                    String newLine = line
-                    while (matcher.find())
-                    {
-                        if (matcher.group(1).equals("enginePath"))
-                            newLine = newLine.replace(matcher.group(), (String) task.inputs.properties.get("directoryPath"))
-                    }
-                    return newLine
-                }
-                )
-                task.destinationDir = new File("${ServerDeployExtension.getServerDeployDirectoryPath(project)}/config")
-
-        }
-
         project.tasks.register("validateConfiguration") {
             Task task ->
                 task.doFirst

From 1da29766d3186acff738706a58b6de7ffab0e69a Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Wed, 17 Sep 2025 07:59:37 -0700
Subject: [PATCH 56/61] Add some messages about configuration cache
 compatibility

---
 .../labkey/gradle/plugin/ApplyLicenses.groovy |  1 +
 .../gradle/plugin/ClientLibraries.groovy      |  1 +
 .../labkey/gradle/plugin/FileModule.groovy    |  6 +---
 .../org/labkey/gradle/plugin/TeamCity.groovy  |  1 +
 .../labkey/gradle/plugin/TestRunner.groovy    | 35 ++++++++++---------
 .../org/labkey/gradle/plugin/Tomcat.groovy    |  2 ++
 6 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy b/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy
index d9c4e0d9..e6c61408 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ApplyLicenses.groovy
@@ -111,6 +111,7 @@ class ApplyLicenses implements Plugin<Project>
                         }
                     }
                 }
+                it.notCompatibleWithConfigurationCache("Needs to inject ArtifactOperations for zipTree usage")
             }
         }
     }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/ClientLibraries.groovy b/src/main/groovy/org/labkey/gradle/plugin/ClientLibraries.groovy
index 0a2e14d2..0889282f 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/ClientLibraries.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/ClientLibraries.groovy
@@ -51,6 +51,7 @@ class ClientLibraries
                     task.dependsOn(project.tasks.processResources)
                     task.dependsOn(project.project(minProjectPath).tasks.named("npmInstall"))
                     task.xmlFiles = getLibXmlFiles(project)
+                    task.notCompatibleWithConfigurationCache("Class ClientLibsCompress needs more input and output properties declared")
             }
 
             project.evaluationDependsOn(minProjectPath)
diff --git a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
index 52b5fcd7..b7849bc3 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
@@ -223,13 +223,9 @@ class FileModule implements Plugin<Project>
                 task.doLast {
                     BuildUtils.updateRestartTriggerFile(project)
                 }
+                task.notCompatibleWithConfigurationCache("Does multiple deletes using project.delete. Should have its own class.")
         }
 
-        project.tasks.named('undeployModule')
-                {
-                    notCompatibleWithConfigurationCache("Need a good way to pick up all the module files and directories. Will likely required its own class with various task outputs as inputs.")
-                }
-
         project.tasks.register("reallyClean") {
             Task task ->
                 task.group = GroupNames.BUILD
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 21bb1f86..6e8b9901 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -280,6 +280,7 @@ class TeamCity extends Tomcat
                         extension.writeStartupProperties('00_modulesInclude.properties',
                                 'ModuleLoader.include;startup=' + String.join(',', includeModules))
                     }
+                    task.notCompatibleWithConfigurationCache("Needs the distribution configuration specified as an input ConfigurableFileCollection")
             }
 
             project.tasks.named("startLabKey").configure {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
index 14dcdf58..d4149139 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
@@ -159,22 +159,25 @@ class TestRunner extends UiTest
 
     private void addAspectJ(Project project)
     {
-        project.tasks.named('compileUiTestJava').configure {doLast {
-            ant.taskdef(
-                resource: "org/aspectj/tools/ant/taskdefs/aspectjTaskdefs.properties",
-                classpath: project.configurations.aspectj.asPath
-            )
-            ant.iajc(
-                destdir: BuildUtils.getBuildDirFile(project,"classes/java/uiTest/").getPath(),
-                source: project.sourceCompatibility,
-                target: project.targetCompatibility,
-                classpath: project.configurations.uiTestRuntimeClasspath.asPath,
-                {
-                    project.sourceSets.uiTest.java.srcDirs.each {
-                        src(path: it)
+        project.tasks.named('compileUiTestJava').configure {it ->
+            it.doLast {
+                ant.taskdef(
+                    resource: "org/aspectj/tools/ant/taskdefs/aspectjTaskdefs.properties",
+                    classpath: project.configurations.aspectj.asPath
+                )
+                ant.iajc(
+                    destdir: BuildUtils.getBuildDirFile(project,"classes/java/uiTest/").getPath(),
+                    source: project.sourceCompatibility,
+                    target: project.targetCompatibility,
+                    classpath: project.configurations.uiTestRuntimeClasspath.asPath,
+                    {
+                        project.sourceSets.uiTest.java.srcDirs.each {
+                            src(path: it)
+                        }
                     }
-                }
-            )
-        }}
+                )
+            }
+            it.notCompatibleWithConfigurationCache("Needs configurations adn sourceSets specified as ConfigurableFileCollection.")
+        }
     }
 }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy b/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
index 63c4814d..f6b4a7ee 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Tomcat.groovy
@@ -58,6 +58,7 @@ class Tomcat implements Plugin<Project>
             StartLabKey task ->
                 task.group = GroupNames.WEB_APPLICATION
                 task.description = "Start the LabKey web application"
+                task.notCompatibleWithConfigurationCache("Needs some properties converted to inputs and outputs")
         }
 
         project.tasks.register("stopLabKey", StopLabKey) {
@@ -71,6 +72,7 @@ class Tomcat implements Plugin<Project>
             StartLabKey task ->
                 task.group = GroupNames.WEB_APPLICATION
                 task.description = "Start the LabKey web application (deprecated: use startLabKey)"
+                task.notCompatibleWithConfigurationCache("Needs some properties converted to inputs and outputs")
         }
 
         project.tasks.register("stopTomcat", StopLabKey) {

From b7b309b2e0e9927891cf92efb4f92cbd3f5d3728 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 22 Sep 2025 07:58:06 -0700
Subject: [PATCH 57/61] Add TODO for possible Antlr plugin usage

---
 src/main/groovy/org/labkey/gradle/plugin/Antlr.groovy | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/Antlr.groovy b/src/main/groovy/org/labkey/gradle/plugin/Antlr.groovy
index 6034919a..6a6052be 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Antlr.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Antlr.groovy
@@ -26,6 +26,7 @@ import org.labkey.gradle.util.GroupNames
 
 /**
  * Used to compile antlr grammars into Java classes using the antlr executable.
+ * TODO: This could be converted to using the Antlr plugin https://docs.gradle.org/9.1.0/userguide/antlr_plugin.html
  */
 class Antlr implements Plugin<Project>
 {

From a121011fd75afcb7fb90c7ba3d33ee0fb9ba3076 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 22 Sep 2025 08:21:04 -0700
Subject: [PATCH 58/61] Remove description property in favor of the default
 project description

---
 .../labkey/gradle/plugin/extension/DistributionExtension.groovy  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
index 77fd1f27..86315974 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/DistributionExtension.groovy
@@ -28,7 +28,6 @@ class DistributionExtension
     public static final String TAR_ARCHIVE_EXTENSION = "tar.gz"
 
     String dir = "${project.rootProject.projectDir}/dist"
-    String description // TODO this is set in various distribution build.gradle files but doesn't seem to be used. Remove?
 
     private Project project
 

From 22491a331038aa6cc37eacf3e8fba9f25c08c447 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 22 Sep 2025 08:21:25 -0700
Subject: [PATCH 59/61] Move static methods back to TeamCityExtension

---
 .../labkey/gradle/plugin/Distribution.groovy  |  7 +-
 .../labkey/gradle/plugin/FileModule.groovy    |  5 +-
 .../org/labkey/gradle/plugin/TeamCity.groovy  |  9 +-
 .../labkey/gradle/plugin/TestRunner.groovy    |  6 +-
 .../plugin/extension/TeamCityExtension.groovy | 75 +++++++++++++++-
 .../plugin/extension/UiTestExtension.groovy   |  5 +-
 .../labkey/gradle/task/InstallRPackage.groovy |  3 +-
 .../labkey/gradle/task/RunTestSuite.groovy    |  3 +-
 .../labkey/gradle/task/SetUpProperties.groovy |  5 +-
 .../org/labkey/gradle/task/StartLabKey.groovy |  7 +-
 .../gradle/task/TeamCityPropertiesTask.groovy | 85 ++-----------------
 .../org/labkey/gradle/util/BuildUtils.groovy  |  7 +-
 12 files changed, 103 insertions(+), 114 deletions(-)

diff --git a/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy b/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
index ea4015fa..9cec6412 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy
@@ -23,16 +23,11 @@ import org.gradle.api.artifacts.ModuleDependency
 import org.gradle.api.artifacts.ProjectDependency
 import org.gradle.api.file.DeleteSpec
 import org.gradle.api.internal.artifacts.dependencies.DefaultProjectDependency
-import org.gradle.api.publish.maven.MavenPublication
 import org.gradle.api.tasks.Delete
 import org.labkey.gradle.plugin.extension.DistributionExtension
-import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
-import org.labkey.gradle.task.ModuleDistribution
-import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
-import org.labkey.gradle.util.PomFileHelper
 import org.labkey.gradle.util.TaskUtils
 
 class Distribution implements Plugin<Project>
@@ -47,7 +42,7 @@ class Distribution implements Plugin<Project>
         // We add the TeamCity extension here if it doesn't exist because we will use the build
         // number property from TeamCity in the distribution artifact names, if present.
         TeamCityExtension teamCityExt  = project.getExtensions().findByType(TeamCityExtension.class)
-        if (TeamCityPropertiesTask.isOnTeamCity(project) && teamCityExt == null)
+        if (TeamCityExtension.isOnTeamCity(project) && teamCityExt == null)
             project.extensions.create("teamCity", TeamCityExtension, project)
 
         if (BuildUtils.getServerProject(project) != null) {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
index b7849bc3..e4f2bc51 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy
@@ -194,12 +194,9 @@ class FileModule implements Plugin<Project>
                     }
                     BuildUtils.updateRestartTriggerFile(project)
                 }
+                task.notCompatibleWithConfigurationCache("Needs its own class to do the two copies (one to staging and one to deploy or possibly two Copy tasks chained together.")
             }
 
-        project.tasks.named('deployModule')
-            {
-                notCompatibleWithConfigurationCache("Needs its own class to do the two copies (one to staging and one to deploy or possibly two Copy tasks chained together.")
-            }
 
 
         project.tasks.register('undeployModule', Delete) {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
index 6e8b9901..216f9513 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TeamCity.groovy
@@ -35,24 +35,19 @@ import org.gradle.api.UnknownTaskException
 import org.gradle.api.file.DeleteSpec
 import org.gradle.api.logging.Logger
 import org.gradle.api.provider.Provider
-import org.gradle.api.tasks.Copy
 import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.JavaExec
 import org.gradle.api.tasks.TaskProvider
-import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.PickDb
 import org.labkey.gradle.task.RunTestSuite
 import org.labkey.gradle.task.TeamCityDbSetup
-import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.task.UndeployModules
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.GroupNames
-import org.labkey.gradle.util.PropertiesUtils
 
 import java.time.Duration
-import java.util.regex.Matcher
 
 /**
  * Creates tasks for TeamCity to run its tests suites based on properties set in a build configuration (particularly for
@@ -101,8 +96,8 @@ class TeamCity extends Tomcat
                 task.dependsOn(project.tasks.jar)
                 task.mainClass.set("org.labkey.test.util.PasswordUtil")
                 task.classpath(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
-                task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
-                task.args("set", TeamCityPropertiesTask.getLabKeyUsername(project), TeamCityPropertiesTask.getLabKeyPassword(project))
+                task.systemProperty("labkey.server", TeamCityExtension.getLabKeyServer(project))
+                task.args("set", TeamCityExtension.getLabKeyUsername(project), TeamCityExtension.getLabKeyPassword(project))
         }
 
         project.tasks.register("cleanTestLogs", Delete) {
diff --git a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
index d4149139..aae0e2a7 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/TestRunner.groovy
@@ -18,8 +18,8 @@ package org.labkey.gradle.plugin
 import org.gradle.api.Project
 import org.gradle.api.Task
 import org.gradle.api.tasks.JavaExec
+import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.task.RunTestSuite
-import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 
@@ -82,7 +82,7 @@ class TestRunner extends UiTest
                 task.description = "Set the password for use in running tests"
                 task.classpath(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
                 task.mainClass.set("org.labkey.test.util.PasswordUtil")
-                task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
+                task.systemProperty("labkey.server", TeamCityExtension.getLabKeyServer(project))
                 task.args("set")
                 task.standardInput = System.in
         }
@@ -95,7 +95,7 @@ class TestRunner extends UiTest
                 task.dependsOn(project.tasks.jar)
                 task.mainClass.set("org.labkey.test.util.PasswordUtil")
                 task.classpath(project.configurations.uiTestRuntimeClasspath, project.tasks.jar)
-                task.systemProperty("labkey.server", TeamCityPropertiesTask.getLabKeyServer(project))
+                task.systemProperty("labkey.server", TeamCityExtension.getLabKeyServer(project))
                 task.args("ensure")
                 task.standardInput = System.in
         }
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
index dabc8604..9d28f27b 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/TeamCityExtension.groovy
@@ -17,7 +17,6 @@ package org.labkey.gradle.plugin.extension
 
 import org.apache.commons.io.FileUtils
 import org.gradle.api.Project
-import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.DatabaseProperties
 
 import java.nio.charset.StandardCharsets
@@ -37,6 +36,78 @@ class TeamCityExtension
         setValidationMessages()
     }
 
+    static boolean isOnTeamCity(Project project)
+    {
+        return project.hasProperty('teamcity')
+    }
+
+    static Object getTeamCityProperty(Project project, String name, Object defaultValue)
+    {
+        if (isOnTeamCity(project))
+            return project.teamcity[name] != null ? project.teamcity[name] : defaultValue
+        else if (project.hasProperty(name))
+            return project.property(name)
+        else
+            return defaultValue
+    }
+
+    static Properties getTeamCityProperties(Project project)
+    {
+        if (isOnTeamCity(project))
+        {
+            def tcProps = new Properties()
+            tcProps.putAll(project.teamcity)
+            return tcProps
+        }
+        else
+            return new Properties()
+    }
+
+    static String getLabKeyServer(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.server", "http://localhost")
+    }
+
+    static String getLabKeyContextPath(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.contextpath", null)
+    }
+
+    static String getLabKeyServerPort(Project project)
+    {
+        return getTeamCityProperty(project, 'tomcat.port', null)
+    }
+
+    static String getLabKeyServerShutdownPort(Project project)
+    {
+        return getTeamCityProperty(project, 'tomcat.shutdown', null)
+    }
+
+    static String getLabKeyServerKeystore(Project project)
+    {
+        return getTeamCityProperty(project, 'labkey.keystore', null)
+    }
+
+    static String getLabKeyServerKeystorePassword(Project project)
+    {
+        return getTeamCityProperty(project, 'labkey.keystore.password', null)
+    }
+
+    static String getLabKeyUsername(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.server.email", "teamcity@labkey.test")
+    }
+
+    static String getLabKeyPassword(Project project)
+    {
+        return getTeamCityProperty(project, "labkey.server.password", "We'reSo\$tr0ng@yekbal1!")
+    }
+
+    static String getTomcatJavaHome(Project project)
+    {
+        return getTeamCityProperty(project, "tomcatJavaHome", System.getenv("JAVA_HOME"))
+    }
+
     Boolean isValidForTestRun()
     {
         return validationMessages.isEmpty()
@@ -145,7 +216,7 @@ class TeamCityExtension
 
     Object getTeamCityProperty(String name, Object defaultValue)
     {
-        TeamCityPropertiesTask.getTeamCityProperty(project, name, defaultValue)
+        getTeamCityProperty(project, name, defaultValue)
     }
 
 
diff --git a/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy b/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy
index 2d38a9e4..5cb23d82 100644
--- a/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy
+++ b/src/main/groovy/org/labkey/gradle/plugin/extension/UiTestExtension.groovy
@@ -18,7 +18,6 @@ package org.labkey.gradle.plugin.extension
 
 import org.gradle.api.GradleException
 import org.gradle.api.Project
-import org.labkey.gradle.task.TeamCityPropertiesTask
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.PropertiesUtils
@@ -36,7 +35,7 @@ class UiTestExtension
     {
         this.project = project
         TeamCityExtension tcExtension = project.extensions.findByType(TeamCityExtension.class)
-        if (TeamCityPropertiesTask.isOnTeamCity(project) && tcExtension == null)
+        if (TeamCityExtension.isOnTeamCity(project) && tcExtension == null)
             this.tcExtension = project.extensions.create("teamCity", TeamCityExtension, project)
     }
 
@@ -87,7 +86,7 @@ class UiTestExtension
         if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null)
         {
             def propertiesFile = project.project(BuildUtils.getTestProjectPath(project.gradle)).file(propertiesFileName)
-            if (TeamCityPropertiesTask.isOnTeamCity(project))
+            if (TeamCityExtension.isOnTeamCity(project))
             {
                 // Load properties from template when running on TeamCity.
                 // These properties control which TeamCity properties are loaded by `RunTestSuite.setTeamCityProperties`
diff --git a/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy b/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy
index c5eb4f0a..f3674b67 100644
--- a/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/InstallRPackage.groovy
@@ -22,6 +22,7 @@ import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.TaskAction
+import org.labkey.gradle.plugin.extension.TeamCityExtension
 
 class InstallRPackage extends DefaultTask
 {
@@ -137,7 +138,7 @@ class InstallRPackage extends DefaultTask
 
     static String getRLibsUserPath(Project project)
     {
-        return TeamCityPropertiesTask.getTeamCityProperty(project, "R_LIBS_USER", System.getenv("R_LIBS_USER"))
+        return TeamCityExtension.getTeamCityProperty(project, "R_LIBS_USER", System.getenv("R_LIBS_USER"))
     }
 
     void installRPackage(String scriptName)
diff --git a/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy b/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy
index 6c74e78a..9d259663 100644
--- a/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/RunTestSuite.groovy
@@ -18,6 +18,7 @@ package org.labkey.gradle.task
 import org.apache.commons.lang3.StringUtils
 import org.gradle.api.tasks.Internal
 import org.labkey.gradle.plugin.TeamCity
+import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.util.DatabaseProperties
 
 /**
@@ -49,7 +50,7 @@ abstract class RunTestSuite extends RunUiTest
 
     protected void setTeamCityProperties()
     {
-        if (TeamCityPropertiesTask.isOnTeamCity(project))
+        if (TeamCityExtension.isOnTeamCity(project))
         {
             systemProperty "teamcity.tests.recentlyFailedTests.file", project.teamcity['teamcity.tests.recentlyFailedTests.file']
             systemProperty "teamcity.build.changedFiles.file", project.teamcity['teamcity.build.changedFiles.file']
diff --git a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
index 6d3b162a..f45762cc 100644
--- a/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/SetUpProperties.groovy
@@ -28,13 +28,12 @@ import org.gradle.api.tasks.InputDirectory
 import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.Internal
 import org.gradle.api.tasks.OutputFile
+import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.DatabaseProperties
 import org.labkey.gradle.util.PropertiesUtils
 
 import javax.inject.Inject
-import java.sql.Driver
-import java.sql.DriverManager
 
 abstract class SetUpProperties extends TeamCityPropertiesTask
 {
@@ -131,7 +130,7 @@ abstract class SetUpProperties extends TeamCityPropertiesTask
     Properties getExtraJdbcProperties()
     {
         def extraJdbcProperties = new Properties()
-        def tcProperties = isOnTeamCity.get() ? getTeamCityProperties(project) : new Properties()
+        def tcProperties = isOnTeamCity.get() ? TeamCityExtension.getTeamCityProperties(project) : new Properties()
         for (Map.Entry entry : tcProperties.entrySet())
         {
             if (entry.getKey().startsWith("extraJdbc"))
diff --git a/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy b/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
index 2132e219..1a174c04 100644
--- a/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/StartLabKey.groovy
@@ -27,6 +27,7 @@ import org.gradle.api.tasks.TaskAction
 import org.labkey.gradle.plugin.Tomcat
 import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
+import org.labkey.gradle.plugin.extension.TeamCityExtension
 import org.labkey.gradle.util.BuildUtils
 
 import java.util.stream.Collectors
@@ -96,7 +97,7 @@ abstract class StartLabKey extends TeamCityPropertiesTask
         optsList.add(project.tomcat.assertionFlag)
         optsList.add("-Ddevmode=${LabKeyExtension.isDevMode(project)}".toString())
         optsList.addAll(project.tomcat.catalinaOpts.split(" "))
-        optsList.add("-Xmx${getTeamCityProperty(project, "Xmx", project.tomcat.maxMemory)}".toString())
+        optsList.add("-Xmx${TeamCityExtension.getTeamCityProperty(project, "Xmx", project.tomcat.maxMemory)}".toString())
         if (project.tomcat.disableRecompileJsp)
             optsList.add("-Dlabkey.disableRecompileJsp=true")
         if (project.tomcat.ignoreModuleSource)
@@ -104,9 +105,9 @@ abstract class StartLabKey extends TeamCityPropertiesTask
         optsList.add(project.tomcat.trustStore)
         optsList.add(project.tomcat.trustStorePassword)
 
-        if (isOnTeamCity(project) && SystemUtils.IS_OS_UNIX)
+        if (TeamCityExtension.isOnTeamCity(project) && SystemUtils.IS_OS_UNIX)
         {
-            optsList.add("-DsequencePipelineEnabled=${getTeamCityProperty(project, "sequencePipelineEnabled", false)}".toString())
+            optsList.add("-DsequencePipelineEnabled=${TeamCityExtension.getTeamCityProperty(project, "sequencePipelineEnabled", false)}".toString())
         }
 
         if (project.hasProperty("extraCatalinaOpts"))
diff --git a/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy b/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
index 8b76308e..dbd28b0b 100644
--- a/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
+++ b/src/main/groovy/org/labkey/gradle/task/TeamCityPropertiesTask.groovy
@@ -5,6 +5,7 @@ import org.gradle.api.Project
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.Optional
+import org.labkey.gradle.plugin.extension.TeamCityExtension
 
 import java.util.function.Function
 
@@ -19,43 +20,43 @@ abstract class TeamCityPropertiesTask extends DefaultTask
     @Optional @Input
     final abstract Property<String> labKeyServerPort = project.objects.property(String).convention(
             tcPropOrDefault(project,
-                    TeamCityPropertiesTask::getLabKeyServerPort,
+                    TeamCityExtension::getLabKeyServerPort,
                 "serverPort", project.hasProperty("useSsl") ? "8443" : "8080"))
 
     @Optional @Input
     final abstract Property<String> contextPath = project.objects.property(String).convention(
             tcPropOrDefault(project,
-                    TeamCityPropertiesTask::getLabKeyContextPath,
+                    TeamCityExtension::getLabKeyContextPath,
                     "contextPath",
                     ""))
 
     @Optional @Input
     final abstract Property<String> shutdownPort = project.objects.property(String).convention(
             tcPropOrDefault(project,
-                    TeamCityPropertiesTask::getLabKeyServerShutdownPort,
+                    TeamCityExtension::getLabKeyServerShutdownPort,
                     "shutdownPort",
                     "8081"))
     @Optional @Input
     final abstract Property<String> keyStore = project.objects.property(String).convention(
             tcPropOrDefault(project,
-                    TeamCityPropertiesTask::getLabKeyServerKeystore,
+                    TeamCityExtension::getLabKeyServerKeystore,
                     "keyStore",
                     "/opt/teamcity-agent/localhost.keystore"))
 
     @Optional @Input
     final abstract Property<String> keyStorePassword = project.objects.property(String).convention(
             tcPropOrDefault(project,
-                    TeamCityPropertiesTask::getLabKeyServerKeystorePassword,
+                    TeamCityExtension::getLabKeyServerKeystorePassword,
                     "keyStorePassword",
                     "changeit"))
 
     @Optional @Input
-    final abstract Property<String> labKeyServer = project.objects.property(String).convention(getLabKeyServer(project))
+    final abstract Property<String> labKeyServer = project.objects.property(String).convention(TeamCityExtension.getLabKeyServer(project))
 
     @Optional @Input
     final abstract Property<String> tomcatJavaHome = project.objects.property(String).convention(
             tcPropOrDefault(project,
-                TeamCityPropertiesTask::getTomcatJavaHome,
+                    TeamCityExtension::getTomcatJavaHome,
                     "tomcatJavaHome",
                     System.getenv("JAVA_HOME")
             )
@@ -73,75 +74,5 @@ abstract class TeamCityPropertiesTask extends DefaultTask
         return value
     }
 
-    static boolean isOnTeamCity(Project project)
-    {
-        return project.hasProperty('teamcity')
-    }
-
-    static Object getTeamCityProperty(Project project, String name, Object defaultValue)
-    {
-        if (isOnTeamCity(project))
-            return project.teamcity[name] != null ? project.teamcity[name] : defaultValue
-        else if (project.hasProperty(name))
-            return project.property(name)
-        else
-            return defaultValue
-    }
-
-    static Properties getTeamCityProperties(Project project)
-    {
-        if (isOnTeamCity(project))
-        {
-            def tcProps = new Properties()
-            tcProps.putAll(project.teamcity)
-            return tcProps
-        }
-        else
-            return new Properties()
-    }
-
-    static String getLabKeyServer(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.server", "http://localhost")
-    }
-
-    static String getLabKeyContextPath(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.contextpath", null)
-    }
-
-    static String getLabKeyServerPort(Project project)
-    {
-        return getTeamCityProperty(project, 'tomcat.port', null)
-    }
 
-    static String getLabKeyServerShutdownPort(Project project)
-    {
-        return getTeamCityProperty(project, 'tomcat.shutdown', null)
-    }
-
-    static String getLabKeyServerKeystore(Project project)
-    {
-        return getTeamCityProperty(project, 'labkey.keystore', null)
-    }
-
-    static String getLabKeyServerKeystorePassword(Project project)
-    {
-        return getTeamCityProperty(project, 'labkey.keystore.password', null)
-    }
-
-    static String getLabKeyUsername(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.server.email", "teamcity@labkey.test")
-    }
-
-    static String getLabKeyPassword(Project project)
-    {
-        return getTeamCityProperty(project, "labkey.server.password", "We'reSo\$tr0ng@yekbal1!")
-    }
-
-    static String getTomcatJavaHome(Project project)
-    {
-        return getTeamCityProperty(project, "tomcatJavaHome", System.getenv("JAVA_HOME"))
-    }
 }
diff --git a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
index 43e80d40..9aa6a709 100644
--- a/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
+++ b/src/main/groovy/org/labkey/gradle/util/BuildUtils.groovy
@@ -33,7 +33,6 @@ import org.labkey.gradle.plugin.extension.LabKeyExtension
 import org.labkey.gradle.plugin.extension.ModuleExtension
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
 import org.labkey.gradle.plugin.extension.TeamCityExtension
-import org.labkey.gradle.task.TeamCityPropertiesTask
 
 import java.nio.charset.StandardCharsets
 import java.nio.file.Files
@@ -262,7 +261,7 @@ class BuildUtils
         if (!project.projectDir.exists() && project.hasProperty("downloadLabKeyModules"))
             reasons.add("Project directory ${project.projectDir} does not exist.")
         String propValue = project.hasProperty(property) ? project.property(property) : null
-        String value = TeamCityPropertiesTask.getTeamCityProperty(project, property, propValue)
+        String value = TeamCityExtension.getTeamCityProperty(project, property, propValue)
         if (value == null)
         {
             reasons.add("Project does not have ${property} property")
@@ -492,8 +491,8 @@ class BuildUtils
     static Properties getStandardVCSProperties(project)
     {
         String buildNumber =
-                (String) TeamCityPropertiesTask.getTeamCityProperty(project, "system.teamcity.agent.dotnet.build_id", // Unique build ID
-                        TeamCityPropertiesTask.getTeamCityProperty(project,"build.number", null))
+                (String) TeamCityExtension.getTeamCityProperty(project, "system.teamcity.agent.dotnet.build_id", // Unique build ID
+                        TeamCityExtension.getTeamCityProperty(project,"build.number", null))
         Properties ret = new Properties()
         if (project.plugins.hasPlugin("org.labkey.versioning"))
         {

From 761bda0a4000a48227b364d2a10cdd90d3eb9fc5 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 22 Sep 2025 11:22:53 -0700
Subject: [PATCH 60/61] Release date and version

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 21da78dc..408b4196 100644
--- a/README.md
+++ b/README.md
@@ -13,9 +13,9 @@ on how to do that, including how to develop and test locally and the versioning
 
 ## Release Notes
 
-### TBD
-*Released*: TBD
-(Earliest compatible LabKey version: TBD)
+### 7.0.0
+*Released*: 22 September 2025
+(Earliest compatible LabKey version: 25.10)
 - Update `PurgeArtifacts` task to be compatible with configuration cache and to work with input files so archived projects can be kept up to date
 - Update dependency versions
 - Update DoThenSetup and its relatives to be compatible with configuration cache

From 3049b6e12a654b8d130ced347295b51b77cfd239 Mon Sep 17 00:00:00 2001
From: labkey-susanh <susanh@labkey.com>
Date: Mon, 22 Sep 2025 11:23:41 -0700
Subject: [PATCH 61/61] Prepare for merge to develop

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 6a1f907e..3ac65c89 100644
--- a/build.gradle
+++ b/build.gradle
@@ -43,7 +43,7 @@ dependencies {
 }
 
 group = 'org.labkey.build'
-project.version = "6.4.0-gradle9-SNAPSHOT"
+project.version = "7.1.0-SNAPSHOT"
 
 gradlePlugin {
     plugins {