diff --git a/.github/workflows/code-scanning.yml b/.github/workflows/code-scanning.yml
index 7dda8c9bd..468f425ae 100644
--- a/.github/workflows/code-scanning.yml
+++ b/.github/workflows/code-scanning.yml
@@ -46,6 +46,9 @@ jobs:
           queries: "" # Default query suite
           packs: github/ccr-${{ matrix.language }}-queries
           config: |
+            paths-ignore:
+              - third-party
+              - third-party-licenses.*.md
             default-setup:
               org:
                 model-packs: [ ${{ github.event.inputs.code_scanning_codeql_packs }} ]
diff --git a/.github/workflows/license-check.yml b/.github/workflows/license-check.yml
index d9cb59fb7..a2638eb1f 100644
--- a/.github/workflows/license-check.yml
+++ b/.github/workflows/license-check.yml
@@ -1,9 +1,22 @@
-# Create a github action that runs the license check script and fails if it exits with a non-zero status
+# Automatically fix license files on PRs that need updates
+# Tries to auto-commit the fix, or comments with instructions if push fails
 
 name: License Check
-on: [push, pull_request]
+on:
+  pull_request:
+    branches:
+      - main  # Only run when PR targets main
+    paths:
+      - "**.go"
+      - go.mod
+      - go.sum
+      - ".github/licenses.tmpl"
+      - "script/licenses*"
+      - "third-party-licenses.*.md"
+      - "third-party/**"
 permissions:
-  contents: read
+  contents: write
+  pull-requests: write
 
 jobs:
   license-check:
@@ -12,10 +25,87 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v6
+        with:
+          ref: ${{ github.head_ref }}
 
       - name: Set up Go
         uses: actions/setup-go@v6
         with:
           go-version-file: "go.mod"
-      - name: check licenses
-        run: ./script/licenses-check
+
+      # actions/setup-go does not setup the installed toolchain to be preferred over the system install,
+      # which causes go-licenses to raise "Package ... does not have module info" errors.
+      # For more information, https://github.com/google/go-licenses/issues/244#issuecomment-1885098633
+      - name: Regenerate licenses
+        env:
+          CI: "true"
+        run: |
+          export GOROOT=$(go env GOROOT)
+          export PATH=${GOROOT}/bin:$PATH
+          ./script/licenses
+
+      - name: Check for changes
+        id: changes
+        continue-on-error: true
+        run: script/licenses-check
+
+      - name: Commit and push fixes
+        if: steps.changes.outcome == 'failure'
+        continue-on-error: true
+        id: push
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add third-party-licenses.*.md third-party/
+          git commit -m "chore: regenerate license files
+
+Auto-generated by license-check workflow"
+          git push
+
+      - name: Check if already commented
+        if: steps.changes.outcome == 'failure' && steps.push.outcome == 'failure'
+        id: check_comment
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const { data: comments } = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number
+            });
+            
+            const alreadyCommented = comments.some(comment => 
+              comment.user.login === 'github-actions[bot]' &&
+              comment.body.includes('## ⚠️ License files need updating')
+            );
+            
+            core.setOutput('already_commented', alreadyCommented ? 'true' : 'false');
+
+      - name: Comment with instructions if cannot push
+        if: steps.changes.outcome == 'failure' && steps.push.outcome == 'failure' && steps.check_comment.outputs.already_commented == 'false'
+        uses: actions/github-script@v7
+        with:
+          script: |
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              body: `## ⚠️ License files need updating
+
+The license files are out of date. I tried to fix them automatically but don't have permission to push to this branch.
+
+**Please run:**
+\`\`\`bash
+script/licenses
+git add third-party-licenses.*.md third-party/
+git commit -m "chore: regenerate license files"
+git push
+\`\`\`
+
+Alternatively, enable "Allow edits by maintainers" in the PR settings so I can fix it automatically.`
+            });
+
+      - name: Fail check if changes needed
+        if: steps.changes.outcome == 'failure'
+        run: exit 1
+
diff --git a/script/licenses b/script/licenses
index 4200316b9..026af7f98 100755
--- a/script/licenses
+++ b/script/licenses
@@ -1,6 +1,39 @@
 #!/bin/bash
+#
+# Generate license files for all platform/arch combinations.
+# This script handles architecture-specific dependency differences by:
+# 1. Generating separate license reports per GOOS/GOARCH combination
+# 2. Grouping identical reports together (comma-separated arch names)
+# 3. Creating an index at the top of each platform file
+# 4. Copying all license files to third-party/
+#
+# Note: third-party/ is a union of all license files across all architectures.
+# This means that license files for dependencies present in only some architectures
+# may still appear in third-party/. This is intentional and ensures compliance.
+#
+# Note: we ignore warnings because we want the command to succeed, however the output should be checked
+#       for any new warnings, and potentially we may need to add license information.
+#
+#       Normally these warnings are packages containing non go code, which may or may not require explicit attribution,
+#       depending on the license.
 
-go install github.com/google/go-licenses@latest
+set -e
+
+# Pinned version for CI reproducibility, latest for local development
+# See: https://github.com/cli/cli/pull/11161
+if [ "$CI" = "true" ]; then
+    go install github.com/google/go-licenses@5348b744d0983d85713295ea08a20cca1654a45e # v2.0.1
+else
+    go install github.com/google/go-licenses@latest
+fi
+
+# actions/setup-go does not setup the installed toolchain to be preferred over the system install,
+# which causes go-licenses to raise "Package ... does not have module info" errors in CI.
+# For more information, https://github.com/google/go-licenses/issues/244#issuecomment-1885098633
+if [ "$CI" = "true" ]; then
+    export GOROOT=$(go env GOROOT)
+    export PATH=${GOROOT}/bin:$PATH
+fi
 
 rm -rf third-party
 mkdir -p third-party
@@ -8,14 +41,129 @@ export TEMPDIR="$(mktemp -d)"
 
 trap "rm -fr ${TEMPDIR}" EXIT
 
-for goos in linux darwin windows ; do
-    # Note: we ignore warnings because we want the command to succeed, however the output should be checked
-    #       for any new warnings, and potentially we may need to add license information. 
-    #
-    #       Normally these warnings are packages containing non go code, which may or may not require explicit attribution,
-    #       depending on the license.
-    GOOS="${goos}" GOFLAGS=-mod=mod go-licenses save ./... --save_path="${TEMPDIR}/${goos}" --force || echo "Ignore warnings"
-    GOOS="${goos}" GOFLAGS=-mod=mod go-licenses report ./... --template .github/licenses.tmpl > third-party-licenses.${goos}.md || echo "Ignore warnings"
-    cp -fR "${TEMPDIR}/${goos}"/* third-party/
+# Cross-platform hash function (works on both Linux and macOS)
+compute_hash() {
+    if command -v md5sum >/dev/null 2>&1; then
+        md5sum | cut -d' ' -f1
+    elif command -v md5 >/dev/null 2>&1; then
+        md5 -q
+    else
+        # Fallback to cksum if neither is available
+        cksum | cut -d' ' -f1
+    fi
+}
+
+# Function to get architectures for a given OS
+get_archs() {
+    case "$1" in
+        linux)   echo "386 amd64 arm64" ;;
+        darwin)  echo "amd64 arm64" ;;
+        windows) echo "386 amd64 arm64" ;;
+    esac
+}
+
+# Generate reports for each platform/arch combination
+for goos in darwin linux windows; do
+    echo "Processing ${goos}..."
+    
+    archs=$(get_archs "$goos")
+    
+    for goarch in $archs; do
+        echo "  Generating for ${goos}/${goarch}..."
+        
+        # Generate the license report for this arch
+        report_file="${TEMPDIR}/${goos}_${goarch}_report.md"
+        GOOS="${goos}" GOARCH="${goarch}" GOFLAGS=-mod=mod go-licenses report ./... --template .github/licenses.tmpl > "${report_file}" 2>/dev/null || echo "  (warnings ignored for ${goos}/${goarch})"
+        
+        # Save licenses to temp directory
+        GOOS="${goos}" GOARCH="${goarch}" GOFLAGS=-mod=mod go-licenses save ./... --save_path="${TEMPDIR}/${goos}_${goarch}" --force 2>/dev/null || echo "  (warnings ignored for ${goos}/${goarch})"
+        
+        # Copy to third-party (accumulate all - union of all architectures for compliance)
+        if [ -d "${TEMPDIR}/${goos}_${goarch}" ]; then
+            cp -fR "${TEMPDIR}/${goos}_${goarch}"/* third-party/ 2>/dev/null || true
+        fi
+        
+        # Extract just the package list (skip header), sort it, and hash it
+        # Use LC_ALL=C for consistent sorting across different systems
+        packages_file="${TEMPDIR}/${goos}_${goarch}_packages.txt"
+        if [ -s "${report_file}" ] && grep -qE '^ - \[' "${report_file}" 2>/dev/null; then
+            grep -E '^ - \[' "${report_file}" | LC_ALL=C sort > "${packages_file}"
+            hash=$(cat "${packages_file}" | compute_hash)
+        else
+            echo "(FAILED TO GENERATE LICENSE REPORT FOR ${goos}/${goarch})" > "${packages_file}"
+            hash="FAILED_${goos}_${goarch}"
+        fi
+        
+        # Store hash for grouping
+        echo "${hash}" > "${TEMPDIR}/${goos}_${goarch}_hash.txt"
+    done
+    
+    # Group architectures with identical reports (deterministic order)
+    # Create groups file: hash -> comma-separated archs
+    groups_file="${TEMPDIR}/${goos}_groups.txt"
+    rm -f "${groups_file}"
+    
+    # Process architectures in order to build groups
+    for goarch in $archs; do
+        hash=$(cat "${TEMPDIR}/${goos}_${goarch}_hash.txt")
+        # Check if we've seen this hash before
+        if grep -q "^${hash}:" "${groups_file}" 2>/dev/null; then
+            # Append to existing group
+            existing=$(grep "^${hash}:" "${groups_file}" | cut -d: -f2)
+            sed -i.bak "s/^${hash}:.*/${hash}:${existing}, ${goarch}/" "${groups_file}"
+            rm -f "${groups_file}.bak"
+        else
+            # New group
+            echo "${hash}:${goarch}" >> "${groups_file}"
+        fi
+    done
+    
+    # Generate the combined report for this platform
+    output_file="third-party-licenses.${goos}.md"
+    
+    cat > "${output_file}" << 'EOF'
+# GitHub MCP Server dependencies
+
+The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
+
+## Table of Contents
+
+EOF
+
+    # Build table of contents (sorted for determinism)
+    # Use LC_ALL=C for consistent sorting across different systems
+    LC_ALL=C sort "${groups_file}" | while IFS=: read -r hash group_archs; do
+        # Create anchor-friendly name
+        anchor=$(echo "${group_archs}" | tr ', ' '-' | tr -s '-')
+        echo "- [${group_archs}](#${anchor})" >> "${output_file}"
+    done
+    
+    echo "" >> "${output_file}"
+    echo "---" >> "${output_file}"
+    echo "" >> "${output_file}"
+    
+    # Add each unique report section (sorted for determinism)
+    # Use LC_ALL=C for consistent sorting across different systems
+    LC_ALL=C sort "${groups_file}" | while IFS=: read -r hash group_archs; do
+        # Get the packages from the first arch in this group
+        first_arch=$(echo "${group_archs}" | cut -d',' -f1 | tr -d ' ')
+        packages=$(cat "${TEMPDIR}/${goos}_${first_arch}_packages.txt")
+        
+        cat >> "${output_file}" << EOF
+## ${group_archs}
+
+The following packages are included for the ${group_archs} architectures.
+
+${packages}
+
+EOF
+    done
+    
+    # Add footer
+    echo "[github/github-mcp-server]: https://github.com/github/github-mcp-server" >> "${output_file}"
+    
+    echo "Generated ${output_file}"
 done
 
+echo "Done! License files generated."
+
diff --git a/script/licenses-check b/script/licenses-check
index 67b567d02..430c8170b 100755
--- a/script/licenses-check
+++ b/script/licenses-check
@@ -1,21 +1,34 @@
 #!/bin/bash
+#
+# Check that license files are up to date.
+# This script regenerates the license files and compares them with the committed versions.
+# If there are differences, it exits with an error.
 
-go install github.com/google/go-licenses@latest
-
-for goos in linux darwin windows ; do
-    # Note: we ignore warnings because we want the command to succeed, however the output should be checked
-    #       for any new warnings, and potentially we may need to add license information. 
-    #
-    #       Normally these warnings are packages containing non go code, which may or may not require explicit attribution,
-    #       depending on the license.
-    GOOS="${goos}" GOFLAGS=-mod=mod go-licenses report ./... --template .github/licenses.tmpl > third-party-licenses.${goos}.copy.md || echo "Ignore warnings"
-    if ! diff -s third-party-licenses.${goos}.copy.md third-party-licenses.${goos}.md; then
-        printf "License check failed.\n\nPlease update the license file by running \`.script/licenses\` and committing the output."
-        rm -f third-party-licenses.${goos}.copy.md
-        exit 1
-    fi
-    rm -f third-party-licenses.${goos}.copy.md
+set -e
+
+# Store original files for comparison
+TEMPDIR="$(mktemp -d)"
+trap "rm -fr ${TEMPDIR}" EXIT
+
+# Save original license markdown files
+for goos in darwin linux windows; do
+    cp "third-party-licenses.${goos}.md" "${TEMPDIR}/"
 done
 
+# Save the state of third-party directory
+cp -r third-party "${TEMPDIR}/third-party.orig"
+
+# Regenerate using the same script
+./script/licenses
+
+# Check for any differences in workspace
+if ! git diff --exit-code --quiet third-party-licenses.*.md third-party/; then
+    echo "License files are out of date:"
+    git diff third-party-licenses.*.md third-party/
+    echo ""
+    printf "\nLicense check failed.\n\nPlease update the license files by running \`./script/licenses\` and committing the output.\n"
+    exit 1
+fi
 
+echo "License check passed for all platforms."
 
diff --git a/third-party-licenses.darwin.md b/third-party-licenses.darwin.md
index 32cdb5b6d..ef8816689 100644
--- a/third-party-licenses.darwin.md
+++ b/third-party-licenses.darwin.md
@@ -2,10 +2,15 @@
 
 The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
 
-## Go Packages
+## Table of Contents
 
-Some packages may only be included on certain architectures or operating systems.
+- [amd64, arm64](#amd64-arm64)
 
+---
+
+## amd64, arm64
+
+The following packages are included for the amd64, arm64 architectures.
 
  - [github.com/aymerick/douceur](https://pkg.go.dev/github.com/aymerick/douceur) ([MIT](https://github.com/aymerick/douceur/blob/v0.2.0/LICENSE))
  - [github.com/fsnotify/fsnotify](https://pkg.go.dev/github.com/fsnotify/fsnotify) ([BSD-3-Clause](https://github.com/fsnotify/fsnotify/blob/v1.9.0/LICENSE))
diff --git a/third-party-licenses.linux.md b/third-party-licenses.linux.md
index 32cdb5b6d..851a70594 100644
--- a/third-party-licenses.linux.md
+++ b/third-party-licenses.linux.md
@@ -2,10 +2,15 @@
 
 The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
 
-## Go Packages
+## Table of Contents
 
-Some packages may only be included on certain architectures or operating systems.
+- [386, amd64, arm64](#386-amd64-arm64)
 
+---
+
+## 386, amd64, arm64
+
+The following packages are included for the 386, amd64, arm64 architectures.
 
  - [github.com/aymerick/douceur](https://pkg.go.dev/github.com/aymerick/douceur) ([MIT](https://github.com/aymerick/douceur/blob/v0.2.0/LICENSE))
  - [github.com/fsnotify/fsnotify](https://pkg.go.dev/github.com/fsnotify/fsnotify) ([BSD-3-Clause](https://github.com/fsnotify/fsnotify/blob/v1.9.0/LICENSE))
diff --git a/third-party-licenses.windows.md b/third-party-licenses.windows.md
index c7e00fb13..f4f8ee42c 100644
--- a/third-party-licenses.windows.md
+++ b/third-party-licenses.windows.md
@@ -2,10 +2,15 @@
 
 The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
 
-## Go Packages
+## Table of Contents
 
-Some packages may only be included on certain architectures or operating systems.
+- [386, amd64, arm64](#386-amd64-arm64)
 
+---
+
+## 386, amd64, arm64
+
+The following packages are included for the 386, amd64, arm64 architectures.
 
  - [github.com/aymerick/douceur](https://pkg.go.dev/github.com/aymerick/douceur) ([MIT](https://github.com/aymerick/douceur/blob/v0.2.0/LICENSE))
  - [github.com/fsnotify/fsnotify](https://pkg.go.dev/github.com/fsnotify/fsnotify) ([BSD-3-Clause](https://github.com/fsnotify/fsnotify/blob/v1.9.0/LICENSE))