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- 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.