fix(config): Improve config-manager.js for MCP server integration

- 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.

.cursor/mcp.json

@@ -5,7 +5,7 @@
 			"args": ["./mcp-server/server.js"],
 			"env": {
 				"ANTHROPIC_API_KEY": "sk-ant-apikeyhere",
-				"PERPLEXITY_API_KEY": "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",
+				"PERPLEXITY_API_KEY": "pplx-apikeyhere",
 				"OPENAI_API_KEY": "sk-proj-1234567890",
 				"GOOGLE_API_KEY": "AIzaSyB1234567890",
 				"GROK_API_KEY": "gsk_1234567890",