feat: enhance database transactions, add Makefiles, and improve Docker setup

- Refactored database batch operations to ensure transaction atomicity and simplify nested structure.
- Added `Makefile` for `knowledge-base` and `llm-gateway` modules to streamline development workflows.
- Simplified `Dockerfile` for `llm-gateway` by removing multi-stage builds and optimizing dependencies.
- Improved code readability in `collection_manager` and `failover` modules with refined logic.
- Minor fixes in `test_server` and Redis health check handling for better diagnostics.

mcp-servers/knowledge-base/Makefile

@@ -0,0 +1,79 @@
+.PHONY: help install install-dev lint lint-fix format type-check test test-cov validate clean run
+
+# Default target
+help:
+	@echo "Knowledge Base MCP Server - Development Commands"
+	@echo ""
+	@echo "Setup:"
+	@echo "  make install       - Install production dependencies"
+	@echo "  make install-dev   - Install development dependencies"
+	@echo ""
+	@echo "Quality Checks:"
+	@echo "  make lint          - Run Ruff linter"
+	@echo "  make lint-fix      - Run Ruff linter with auto-fix"
+	@echo "  make format        - Format code with Ruff"
+	@echo "  make type-check    - Run mypy type checker"
+	@echo ""
+	@echo "Testing:"
+	@echo "  make test          - Run pytest"
+	@echo "  make test-cov      - Run pytest with coverage"
+	@echo ""
+	@echo "All-in-one:"
+	@echo "  make validate      - Run lint, type-check, and tests"
+	@echo ""
+	@echo "Running:"
+	@echo "  make run           - Run the server locally"
+	@echo ""
+	@echo "Cleanup:"
+	@echo "  make clean         - Remove cache and build artifacts"
+
+# Setup
+install:
+	@echo "Installing production dependencies..."
+	@uv pip install -e .
+
+install-dev:
+	@echo "Installing development dependencies..."
+	@uv pip install -e ".[dev]"
+
+# Quality checks
+lint:
+	@echo "Running Ruff linter..."
+	@uv run ruff check .
+
+lint-fix:
+	@echo "Running Ruff linter with auto-fix..."
+	@uv run ruff check --fix .
+
+format:
+	@echo "Formatting code..."
+	@uv run ruff format .
+
+type-check:
+	@echo "Running mypy..."
+	@uv run mypy . --ignore-missing-imports
+
+# Testing
+test:
+	@echo "Running tests..."
+	@uv run pytest tests/ -v
+
+test-cov:
+	@echo "Running tests with coverage..."
+	@uv run pytest tests/ -v --cov=. --cov-report=term-missing --cov-report=html
+
+# All-in-one validation
+validate: lint type-check test
+	@echo "All validations passed!"
+
+# Running
+run:
+	@echo "Starting Knowledge Base server..."
+	@uv run python server.py
+
+# Cleanup
+clean:
+	@echo "Cleaning up..."
+	@rm -rf __pycache__ .pytest_cache .mypy_cache .ruff_cache .coverage htmlcov
+	@find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
+	@find . -type f -name "*.pyc" -delete 2>/dev/null || true

mcp-servers/knowledge-base/collection_manager.py

@@ -328,7 +328,7 @@ class CollectionManager:
                 "source_path": chunk.source_path or source_path,
                 "start_line": chunk.start_line,
                 "end_line": chunk.end_line,
-                "file_type": (chunk.file_type or file_type).value if (chunk.file_type or file_type) else None,
+                "file_type": effective_file_type.value if (effective_file_type := chunk.file_type or file_type) else None,
             }
             embeddings_data.append((
                 chunk.content,

mcp-servers/knowledge-base/database.py

@@ -284,9 +284,8 @@ class DatabaseManager:
             )
 
         try:
-            async with self.acquire() as conn:
+            async with self.acquire() as conn, conn.transaction():
                 # Wrap in transaction for all-or-nothing batch semantics
-                async with conn.transaction():
                 for project_id, collection, content, embedding, chunk_type, metadata in embeddings:
                     content_hash = self.compute_content_hash(content)
                     source_path = metadata.get("source_path")
@@ -566,9 +565,8 @@ class DatabaseManager:
             )
 
         try:
-            async with self.acquire() as conn:
+            async with self.acquire() as conn, conn.transaction():
                 # Use transaction for atomic replace
-                async with conn.transaction():
                 # First, delete existing embeddings for this source
                 delete_result = await conn.execute(
                     """

mcp-servers/knowledge-base/server.py

@@ -193,7 +193,7 @@ async def health_check() -> dict[str, Any]:
     # Check Redis cache (non-critical - degraded without it)
     try:
         if _embeddings and _embeddings._redis:
-            await _embeddings._redis.ping()
+            await _embeddings._redis.ping()  # type: ignore[misc]
             status["dependencies"]["redis"] = "connected"
         else:
             status["dependencies"]["redis"] = "not initialized"

mcp-servers/knowledge-base/tests/test_server.py

@@ -1,8 +1,7 @@
 """Tests for server module and MCP tools."""
 
-import json
 from datetime import UTC, datetime
-from unittest.mock import AsyncMock, MagicMock, patch
+from unittest.mock import AsyncMock, MagicMock
 
 import pytest
 from fastapi.testclient import TestClient

mcp-servers/llm-gateway/Dockerfile

@@ -1,39 +1,25 @@
 # Syndarix LLM Gateway MCP Server
-# Multi-stage build for minimal image size
+FROM python:3.12-slim
 
-# Build stage
+WORKDIR /app
-FROM python:3.12-slim AS builder
+
+# Install system dependencies (needed for tiktoken regex compilation)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
 
 # Install uv for fast package management
-COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
 
-WORKDIR /app
+# Copy project files
-
-# Copy dependency files
 COPY pyproject.toml ./
+COPY *.py ./
 
-# Create virtual environment and install dependencies
+# Install dependencies to system Python
-RUN uv venv /app/.venv
+RUN uv pip install --system --no-cache .
-ENV PATH="/app/.venv/bin:$PATH"
-RUN uv pip install -e .
-
-# Runtime stage
-FROM python:3.12-slim AS runtime
 
 # Create non-root user for security
-RUN groupadd --gid 1000 appgroup && \
+RUN useradd --create-home --shell /bin/bash appuser
-    useradd --uid 1000 --gid appgroup --shell /bin/bash --create-home appuser
-
-WORKDIR /app
-
-# Copy virtual environment from builder
-COPY --from=builder /app/.venv /app/.venv
-ENV PATH="/app/.venv/bin:$PATH"
-
-# Copy application code
-COPY --chown=appuser:appgroup . .
-
-# Switch to non-root user
 USER appuser
 
 # Environment variables
@@ -47,7 +33,7 @@ EXPOSE 8001
 
 # Health check
 HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
-    CMD python -c "import httpx; httpx.get('http://localhost:8001/health').raise_for_status()" || exit 1
+    CMD python -c "import httpx; httpx.get('http://localhost:8001/health').raise_for_status()"
 
 # Run the server
 CMD ["python", "server.py"]

mcp-servers/llm-gateway/Makefile

@@ -0,0 +1,79 @@
+.PHONY: help install install-dev lint lint-fix format type-check test test-cov validate clean run
+
+# Default target
+help:
+	@echo "LLM Gateway MCP Server - Development Commands"
+	@echo ""
+	@echo "Setup:"
+	@echo "  make install       - Install production dependencies"
+	@echo "  make install-dev   - Install development dependencies"
+	@echo ""
+	@echo "Quality Checks:"
+	@echo "  make lint          - Run Ruff linter"
+	@echo "  make lint-fix      - Run Ruff linter with auto-fix"
+	@echo "  make format        - Format code with Ruff"
+	@echo "  make type-check    - Run mypy type checker"
+	@echo ""
+	@echo "Testing:"
+	@echo "  make test          - Run pytest"
+	@echo "  make test-cov      - Run pytest with coverage"
+	@echo ""
+	@echo "All-in-one:"
+	@echo "  make validate      - Run lint, type-check, and tests"
+	@echo ""
+	@echo "Running:"
+	@echo "  make run           - Run the server locally"
+	@echo ""
+	@echo "Cleanup:"
+	@echo "  make clean         - Remove cache and build artifacts"
+
+# Setup
+install:
+	@echo "Installing production dependencies..."
+	@uv pip install -e .
+
+install-dev:
+	@echo "Installing development dependencies..."
+	@uv pip install -e ".[dev]"
+
+# Quality checks
+lint:
+	@echo "Running Ruff linter..."
+	@uv run ruff check .
+
+lint-fix:
+	@echo "Running Ruff linter with auto-fix..."
+	@uv run ruff check --fix .
+
+format:
+	@echo "Formatting code..."
+	@uv run ruff format .
+
+type-check:
+	@echo "Running mypy..."
+	@uv run mypy . --ignore-missing-imports
+
+# Testing
+test:
+	@echo "Running tests..."
+	@uv run pytest tests/ -v
+
+test-cov:
+	@echo "Running tests with coverage..."
+	@uv run pytest tests/ -v --cov=. --cov-report=term-missing --cov-report=html
+
+# All-in-one validation
+validate: lint type-check test
+	@echo "All validations passed!"
+
+# Running
+run:
+	@echo "Starting LLM Gateway server..."
+	@uv run python server.py
+
+# Cleanup
+clean:
+	@echo "Cleaning up..."
+	@rm -rf __pycache__ .pytest_cache .mypy_cache .ruff_cache .coverage htmlcov
+	@find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
+	@find . -type f -name "*.pyc" -delete 2>/dev/null || true

mcp-servers/llm-gateway/failover.py

@@ -110,9 +110,8 @@ class CircuitBreaker:
         """
         if self._state == CircuitState.OPEN:
             time_in_open = time.time() - self._stats.state_changed_at
-            if time_in_open >= self.recovery_timeout:
+            # Double-check state after time calculation (for thread safety)
-                # Only transition if still in OPEN state (double-check)
+            if time_in_open >= self.recovery_timeout and self._state == CircuitState.OPEN:
-                if self._state == CircuitState.OPEN:
                 self._transition_to(CircuitState.HALF_OPEN)
                 logger.info(
                     f"Circuit {self.name} transitioned to HALF_OPEN "