Refactor settings management to use ~/.claude-mem/settings.json

- Updated paths in troubleshooting documentation to reflect new settings file location.
- Modified diagnostics and reference files to read from ~/.claude-mem/settings.json.
- Introduced getWorkerPort utility for cleaner worker port retrieval.
- Enhanced ChromaSync and SDKAgent to load Python version and Claude path from settings.
- Updated SettingsRoutes to validate new settings: CLAUDE_MEM_LOG_LEVEL and CLAUDE_MEM_PYTHON_VERSION.
- Added early-settings module to load settings for logger and other early-stage modules.
- Adjusted logger to use early-loaded log level setting.
- Refactored paths to utilize early-loaded data directory setting.

src/utils/logger.ts

@@ -3,6 +3,8 @@
  * Provides readable, traceable logging with correlation IDs and data flow tracking
  */
 
+import { loadEarlySetting } from '../shared/early-settings.js';
+
 export enum LogLevel {
   DEBUG = 0,
   INFO = 1,
@@ -26,7 +28,7 @@ class Logger {
 
   constructor() {
     // Parse log level from environment
-    const envLevel = process.env.CLAUDE_MEM_LOG_LEVEL?.toUpperCase() || 'INFO';
+    const envLevel = loadEarlySetting('CLAUDE_MEM_LOG_LEVEL', 'INFO').toUpperCase();
     this.level = LogLevel[envLevel as keyof typeof LogLevel] ?? LogLevel.INFO;
 
     // Disable colors when output is not a TTY (e.g., PM2 logs)