fix: eliminate all skipped E2E tests and resolve external process failures

[Copilot]

This PR fixes critical E2E test failures and implements comprehensive development infrastructure improvements to achieve zero skipped tests and resolve external process conflicts.

Key Fixes

FastMCP Async Architecture: Replaced the threading approach with FastMCP's async stdio runner to eliminate event loop conflicts. The server now uses await self.mcp.run_stdio_async() instead of nested asyncio.run() calls, resolving the core issue causing external process test failures.

MCP Tool Parameter Validation: Fixed parameter validation issues where tests were using incorrect parameter names (isError → is_error) and corrected tool parameter mapping throughout the E2E test suite.

E2E Test Infrastructure: Removed all @pytest.mark.skip decorators from E2E tests, enabling full Redis integration and external process testing. All 33 E2E tests now run and pass successfully.

Architecture Improvements

The server architecture has been significantly improved to handle external process execution properly:

# Before: Threading approach with event loop conflicts
def run_server():
    asyncio.run(server.run())  # Nested event loop issues

# After: FastMCP async stdio runner
async def run(self):
    await self.mcp.run_stdio_async()  # Proper async handling

E2E Test Results

• 33/33 E2E tests now run and pass (9 + 10 + 6 + 8 across 4 test files)
• Zero skipped tests achieved in E2E test suite
• External process testing fully functional with proper session handling
• Redis integration enabled with correct parameter mapping
• Source ID extraction and client session handling implemented

Development Infrastructure

Added comprehensive .claude folder structure with:

• Quality gate commands for automated validation
• PR preparation workflows following established conventions
• Planning methodology and development context
• Reusable command patterns for common tasks

Quality Improvements

Cleaned up repository hygiene by removing unwanted files (.DS_Store, __pycache__ directories) that were incorrectly committed, ensuring proper .gitignore compliance.

This PR transforms the E2E testing infrastructure from a broken state with multiple skipped tests to a fully functional test suite that properly validates MCP server functionality in real-world scenarios, including Claude Desktop integration patterns.

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