- Fixed MCP server initialization warnings by refactoring config-manager.js to handle missing project roots silently during startup
- Added project root tracking (loadedConfigRoot) to improve config caching and prevent unnecessary reloads
- Modified _loadAndValidateConfig to return defaults without warnings when no explicitRoot provided
- Improved getConfig to only update cache when loading config with a specific project root
- Ensured warning messages still appear when explicitly specified roots have missing/invalid configs
- Prevented console output during MCP startup that was causing JSON parsing errors
- Verified parse_prd and other MCP tools still work correctly with the new config loading approach.
- Replaces test perplexity api key in mcp.json and rolls it. It's invalid now.
