Claude/refactor directory structure 011 c us sd tp bi mf1 eiq b hx zr m

.bumpversion.toml

@@ -33,7 +33,7 @@ search = 'version = "{current_version}"'
 replace = 'version = "{new_version}"'
 
 [[tool.bumpversion.files]]
-filename = "src/__version__.py"
+filename = "src/codebase_rag/__version__.py"
 search = '__version__ = "{current_version}"'
 replace = '__version__ = "{new_version}"'
 

.github/workflows/docker-build.yml

@@ -30,7 +30,7 @@ jobs:
           echo "pyproject.toml version: $PROJECT_VERSION"
 
           # Get version from __version__.py
-          VERSION_PY=$(grep '__version__ = ' src/__version__.py | cut -d'"' -f2)
+          VERSION_PY=$(grep '__version__ = ' src/codebase_rag/__version__.py | cut -d'"' -f2)
           echo "__version__.py version: $VERSION_PY"
 
           # Validate Python version file
@@ -70,7 +70,7 @@ jobs:
           bun-version: latest
 
       - name: Build Frontend
-        run: ./build-frontend.sh
+        run: ./scripts/build-frontend.sh
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
@@ -121,7 +121,7 @@ jobs:
           bun-version: latest
 
       - name: Build Frontend
-        run: ./build-frontend.sh
+        run: ./scripts/build-frontend.sh
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
@@ -172,7 +172,7 @@ jobs:
           bun-version: latest
 
       - name: Build Frontend
-        run: ./build-frontend.sh
+        run: ./scripts/build-frontend.sh
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3

.github/workflows/docs-deploy.yml

@@ -70,4 +70,4 @@ jobs:
       - name: Notify deployment
         run: |
           echo "📚 Documentation deployed successfully!"
-          echo "🔗 URL: https://code-graph.vantagecraft.dev"
+          echo "🔗 URL: https://vantagecraft.dev/docs/code-graph/"

Dockerfile

@@ -50,10 +50,7 @@ RUN --mount=type=cache,target=/root/.cache/uv \
 
 # Copy application source code for local package installation
 COPY pyproject.toml README.md ./
-COPY api ./api
-COPY core ./core
-COPY services ./services
-COPY mcp_tools ./mcp_tools
+COPY src ./src
 COPY *.py ./
 
 # Install local package (without dependencies, already installed)
@@ -95,15 +92,15 @@ COPY --from=builder /usr/local/bin/uvicorn /usr/local/bin/
 COPY --chown=appuser:appuser . .
 
 # Copy pre-built frontend (if exists)
-# Run ./build-frontend.sh before docker build to generate frontend/dist
+# Run ./scripts/build-frontend.sh before docker build to generate frontend/dist
 # If frontend/dist doesn't exist, the app will run as API-only (no web UI)
 RUN if [ -d frontend/dist ]; then \
         mkdir -p static && \
         cp -r frontend/dist/* static/ && \
         echo "✅ Frontend copied to static/"; \
     else \
         echo "⚠️  No frontend/dist found - running as API-only"; \
-        echo "   Run ./build-frontend.sh to build frontend"; \
+        echo "   Run ./scripts/build-frontend.sh to build frontend"; \
     fi
 
 # Switch to non-root user
@@ -129,6 +126,6 @@ EXPOSE 8000 8080
 HEALTHCHECK --interval=30s --timeout=10s --start-period=40s --retries=3 \
     CMD curl -f http://localhost:8080/api/v1/health || exit 1
 
-# Default command - starts HTTP API (not MCP)
-# For MCP service, run on host: python start_mcp.py
-CMD ["python", "start.py"]
+# Default command - starts both MCP and Web services (dual-port mode)
+# Alternative: python -m codebase_rag --mcp (MCP only) or --web (Web only)
+CMD ["python", "-m", "codebase_rag"]

docker/Dockerfile.base

@@ -2,7 +2,7 @@
 # Base Docker image for Code Graph Knowledge System
 #
 # IMPORTANT: Frontend MUST be pre-built before docker build:
-#   ./build-frontend.sh
+#   ./scripts/build-frontend.sh
 #
 # This Dockerfile expects frontend/dist/ to exist
 
@@ -53,7 +53,7 @@ COPY --chown=appuser:appuser services ./services
 COPY --chown=appuser:appuser mcp_tools ./mcp_tools
 COPY --chown=appuser:appuser start.py start_mcp.py mcp_server.py config.py main.py ./
 
-# Copy pre-built frontend (MUST exist - run ./build-frontend.sh first)
+# Copy pre-built frontend (MUST exist - run ./scripts/build-frontend.sh first)
 COPY --chown=appuser:appuser frontend/dist ./static
 
 USER appuser

docker/Dockerfile.full

@@ -2,7 +2,7 @@
 # Full Docker image - All features (LLM + Embedding required)
 #
 # IMPORTANT: Frontend MUST be pre-built before docker build:
-#   ./build-frontend.sh
+#   ./scripts/build-frontend.sh
 #
 # This Dockerfile expects frontend/dist/ to exist
 
@@ -48,13 +48,9 @@ COPY --from=builder /usr/local/lib/python3.13/site-packages /usr/local/lib/pytho
 COPY --from=builder /usr/local/bin/uvicorn /usr/local/bin/
 
 # Copy application code
-COPY --chown=appuser:appuser api ./api
-COPY --chown=appuser:appuser core ./core
-COPY --chown=appuser:appuser services ./services
-COPY --chown=appuser:appuser mcp_tools ./mcp_tools
-COPY --chown=appuser:appuser start.py start_mcp.py mcp_server.py config.py main.py ./
+COPY --chown=appuser:appuser src ./src
 
-# Copy pre-built frontend (MUST exist - run ./build-frontend.sh first)
+# Copy pre-built frontend (MUST exist - run ./scripts/build-frontend.sh first)
 COPY --chown=appuser:appuser frontend/dist ./static
 
 USER appuser
@@ -67,4 +63,4 @@ HEALTHCHECK --interval=30s --timeout=10s --start-period=40s --retries=3 \
     CMD curl -f http://localhost:8080/api/v1/health || exit 1
 
 # Start application (dual-port mode)
-CMD ["python", "main.py"]
+CMD ["python", "-m", "codebase_rag"]

docker/Dockerfile.minimal

@@ -2,7 +2,7 @@
 # Minimal Docker image - Code Graph only (No LLM required)
 #
 # IMPORTANT: Frontend MUST be pre-built before docker build:
-#   ./build-frontend.sh
+#   ./scripts/build-frontend.sh
 #
 # This Dockerfile expects frontend/dist/ to exist
 
@@ -48,13 +48,9 @@ COPY --from=builder /usr/local/lib/python3.13/site-packages /usr/local/lib/pytho
 COPY --from=builder /usr/local/bin/uvicorn /usr/local/bin/
 
 # Copy application code
-COPY --chown=appuser:appuser api ./api
-COPY --chown=appuser:appuser core ./core
-COPY --chown=appuser:appuser services ./services
-COPY --chown=appuser:appuser mcp_tools ./mcp_tools
-COPY --chown=appuser:appuser start.py start_mcp.py mcp_server.py config.py main.py ./
+COPY --chown=appuser:appuser src ./src
 
-# Copy pre-built frontend (MUST exist - run ./build-frontend.sh first)
+# Copy pre-built frontend (MUST exist - run ./scripts/build-frontend.sh first)
 COPY --chown=appuser:appuser frontend/dist ./static
 
 USER appuser
@@ -67,4 +63,4 @@ HEALTHCHECK --interval=30s --timeout=10s --start-period=40s --retries=3 \
     CMD curl -f http://localhost:8080/api/v1/health || exit 1
 
 # Start application (dual-port mode)
-CMD ["python", "main.py"]
+CMD ["python", "-m", "codebase_rag"]

docker/Dockerfile.standard

@@ -2,7 +2,7 @@
 # Standard Docker image - Code Graph + Memory Store (Embedding required)
 #
 # IMPORTANT: Frontend MUST be pre-built before docker build:
-#   ./build-frontend.sh
+#   ./scripts/build-frontend.sh
 #
 # This Dockerfile expects frontend/dist/ to exist
 
@@ -48,13 +48,9 @@ COPY --from=builder /usr/local/lib/python3.13/site-packages /usr/local/lib/pytho
 COPY --from=builder /usr/local/bin/uvicorn /usr/local/bin/
 
 # Copy application code
-COPY --chown=appuser:appuser api ./api
-COPY --chown=appuser:appuser core ./core
-COPY --chown=appuser:appuser services ./services
-COPY --chown=appuser:appuser mcp_tools ./mcp_tools
-COPY --chown=appuser:appuser start.py start_mcp.py mcp_server.py config.py main.py ./
+COPY --chown=appuser:appuser src ./src
 
-# Copy pre-built frontend (MUST exist - run ./build-frontend.sh first)
+# Copy pre-built frontend (MUST exist - run ./scripts/build-frontend.sh first)
 COPY --chown=appuser:appuser frontend/dist ./static
 
 USER appuser
@@ -67,4 +63,4 @@ HEALTHCHECK --interval=30s --timeout=10s --start-period=40s --retries=3 \
     CMD curl -f http://localhost:8080/api/v1/health || exit 1
 
 # Start application (dual-port mode)
-CMD ["python", "main.py"]
+CMD ["python", "-m", "codebase_rag"]

docs/api/mcp-tools.md

@@ -30,7 +30,7 @@ The MCP server provides AI assistants (like Claude Desktop, VS Code with MCP, et
 
 ```bash
 # Using start script
-python start_mcp.py
+python -m codebase_rag --mcp
 
 # Using uv (recommended)
 uv run mcp_client

docs/api/python-sdk.md

@@ -106,12 +106,12 @@ OPENROUTER_MODEL=anthropic/claude-3-opus
 ### Import Services
 
 ```python
-from services.neo4j_knowledge_service import Neo4jKnowledgeService
-from services.memory_store import MemoryStore, memory_store
-from services.graph_service import Neo4jGraphService, graph_service
-from services.code_ingestor import CodeIngestor, get_code_ingestor
-from services.task_queue import TaskQueue, task_queue
-from config import settings
+from src.codebase_rag.services.knowledge import Neo4jKnowledgeService
+from src.codebase_rag.services.memory import MemoryStore, memory_store
+from src.codebase_rag.services.code import Neo4jGraphService, graph_service
+from src.codebase_rag.services.code import CodeIngestor, get_code_ingestor
+from src.codebase_rag.services.tasks import TaskQueue, task_queue
+from src.codebase_rag.config import settings
 ```
 
 ### Service Initialization Pattern
@@ -148,7 +148,7 @@ Primary service for knowledge graph operations with LlamaIndex integration.
 ### Initialization
 
 ```python
-from services.neo4j_knowledge_service import Neo4jKnowledgeService
+from src.codebase_rag.services.knowledge import Neo4jKnowledgeService
 
 # Create instance
 knowledge_service = Neo4jKnowledgeService()
@@ -405,7 +405,7 @@ Project memory persistence for AI agents.
 ### Initialization
 
 ```python
-from services.memory_store import memory_store
+from src.codebase_rag.services.memory import memory_store
 
 # Initialize (async)
 await memory_store.initialize()
@@ -627,7 +627,7 @@ Low-level Neo4j graph operations.
 ### Initialization
 
 ```python
-from services.graph_service import graph_service
+from src.codebase_rag.services.code import graph_service
 
 # Connect to Neo4j
 await graph_service.connect()
@@ -791,8 +791,8 @@ Repository code ingestion service.
 ### Initialization
 
 ```python
-from services.code_ingestor import get_code_ingestor
-from services.graph_service import graph_service
+from src.codebase_rag.services.code import get_code_ingestor
+from src.codebase_rag.services.code import graph_service
 
 # Initialize graph service first
 await graph_service.connect()
@@ -882,7 +882,7 @@ Asynchronous task queue management.
 ### Initialization
 
 ```python
-from services.task_queue import task_queue, TaskStatus
+from src.codebase_rag.services.tasks import task_queue, TaskStatus
 
 # Start task queue
 await task_queue.start()
@@ -921,7 +921,7 @@ async def submit_task(
 
 **Example**:
 ```python
-from services.task_processors import process_document_task
+from src.codebase_rag.services.tasks import process_document_task
 
 task_id = await task_queue.submit_task(
     task_func=process_document_task,
@@ -1005,7 +1005,7 @@ def get_queue_stats() -> Dict[str, int]:
 Access configuration settings.
 
 ```python
-from config import settings
+from src.codebase_rag.config import settings
 
 # Neo4j settings
 print(settings.neo4j_uri)
@@ -1034,7 +1034,7 @@ print(settings.top_k)
 ### Get Current Model Info
 
 ```python
-from config import get_current_model_info
+from src.codebase_rag.config import get_current_model_info
 
 model_info = get_current_model_info()
 print(f"LLM: {model_info['llm']}")
@@ -1049,7 +1049,7 @@ print(f"Embedding: {model_info['embedding']}")
 
 ```python
 import asyncio
-from services.neo4j_knowledge_service import Neo4jKnowledgeService
+from src.codebase_rag.services.knowledge import Neo4jKnowledgeService
 
 async def main():
     # Initialize service
@@ -1087,7 +1087,7 @@ asyncio.run(main())
 
 ```python
 import asyncio
-from services.memory_store import memory_store
+from src.codebase_rag.services.memory import memory_store
 
 async def main():
     # Initialize
@@ -1128,9 +1128,9 @@ asyncio.run(main())
 
 ```python
 import asyncio
-from services.graph_service import graph_service
-from services.code_ingestor import get_code_ingestor
-from services.git_utils import git_utils
+from src.codebase_rag.services.code import graph_service
+from src.codebase_rag.services.code import get_code_ingestor
+from src.codebase_rag.services.git_utils import git_utils
 
 async def main():
     # Connect to Neo4j
@@ -1178,8 +1178,8 @@ asyncio.run(main())
 
 ```python
 import asyncio
-from services.task_queue import task_queue, TaskStatus
-from services.task_processors import process_document_task
+from src.codebase_rag.services.tasks import task_queue, TaskStatus
+from src.codebase_rag.services.tasks import process_document_task
 
 async def main():
     # Start task queue
@@ -1318,7 +1318,7 @@ result = await session.run("MATCH (n) RETURN n LIMIT 10")
 ### 4. Set Appropriate Timeouts
 
 ```python
-from config import settings
+from src.codebase_rag.config import settings
 
 # Adjust timeouts for large operations
 settings.operation_timeout = 300  # 5 minutes
@@ -1439,7 +1439,7 @@ for item in items:
 
 ```python
 # 60x faster for updates
-from services.git_utils import git_utils
+from src.codebase_rag.services.git_utils import git_utils
 
 if git_utils.is_git_repo(repo_path):
     changed_files = git_utils.get_changed_files(repo_path)

docs/architecture/components.md

@@ -1482,7 +1482,7 @@ Critical for avoiding circular dependencies:
 
 ```python
 # 1. Configuration (no dependencies)
-from config import settings
+from src.codebase_rag.config import settings
 
 # 2. Storage layer (no app dependencies)
 neo4j_connection = Neo4jGraphStore(...)
@@ -1555,7 +1555,7 @@ class Settings(BaseSettings):
 
 Components access configuration:
 ```python
-from config import settings
+from src.codebase_rag.config import settings
 
 # Use in service
 self.timeout = settings.operation_timeout