ROOT CAUSE: Asyncio event loop contamination between MCP server and SerenaAgent
was causing intermittent deadlocks. MCP server runs in its own asyncio loop,
but SerenaAgent creates coroutines that leak into the MCP context, leading to
unawaited coroutines and eventual event loop blocking.
SOLUTION: Complete process isolation with clean architecture
Process Isolation Changes:
- Add ProcessIsolatedSerenaAgent wrapper that runs SerenaAgent in separate process
- Implement JSON-RPC based IPC for communication between MCP server and agent
- Add SerenaAgentWorker class to handle requests in the isolated process
- Centralize error handling in _make_request_with_result() helper method
- Use serena_config.tool_timeout instead of hardcoded timeout parameters
Architecture Improvements:
- Define ToolProtocol interface for clean tool contracts
- Implement ProcessIsolatedTool with complete Tool interface (apply + apply_ex)
- Remove hacky make_process_isolated_tool function - use single make_tool path
- Eliminate inheritance abuse - ProcessIsolatedTool implements protocol cleanly
- Preserve full docstring parsing functionality through process boundary
MCP Server Updates:
- Update start_mcp_server() to use process isolation by default
- Maintain backward compatibility with create_mcp_server_and_agent()
- Retrieve tool metadata from isolated process for proper MCP tool creation
- Ensure proper process lifecycle management in server lifespan handlers
Key Benefits:
- Prevents asyncio contamination deadlocks completely
- Maintains full docstring parsing and parameter schema generation
- Clean protocol-based architecture with no inheritance hacks
- Centralized configuration-driven timeout handling
- All tools implement consistent apply_ex interface
- Process isolation is transparent to MCP clients
This fix ensures that MCP symbolic tools no longer create deadlocks
1. Use all gitignore files in SerenaAgent, not just top level
2. Listing and file finding tools now can find all non-ignored files (previously they would only find code files)
3. Read and edit tools will raise an error on attempting to operate on an ignored file or a path outside the project root
- Update Eclipse JDTLS to vscode-java v1.42.0 with Java 21.0.7 JRE
- Update Kotlin language server dependencies to use Java 21
- Update test Maven project to use Java 21 compiler settings
- Update runtime configuration from JavaSE-17 to JavaSE-21
- Update dependency versions: lombok 1.18.36, launcher 1.7.0
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
Michael Panchenko