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.

README.md

@@ -306,18 +306,42 @@ See [CHANGELOG.md](CHANGELOG.md) for complete version history.
 
 ## Configuration
 
-**Model Selection:**
+Settings are managed in `~/.claude-mem/settings.json`. The file is auto-created with defaults on first run.
+
+**Available Settings:**
+
+| Setting | Default | Description |
+|---------|---------|-------------|
+| `CLAUDE_MEM_MODEL` | `claude-haiku-4-5` | AI model for observations |
+| `CLAUDE_MEM_WORKER_PORT` | `37777` | Worker service port |
+| `CLAUDE_MEM_DATA_DIR` | `~/.claude-mem` | Data directory location |
+| `CLAUDE_MEM_LOG_LEVEL` | `INFO` | Log verbosity (DEBUG, INFO, WARN, ERROR, SILENT) |
+| `CLAUDE_MEM_PYTHON_VERSION` | `3.13` | Python version for chroma-mcp |
+| `CLAUDE_CODE_PATH` | _(auto-detect)_ | Path to Claude executable |
+| `CLAUDE_MEM_CONTEXT_OBSERVATIONS` | `50` | Number of observations to inject at SessionStart |
+
+**Settings Management:**
 
 ```bash
+# Edit settings via CLI helper
 ./claude-mem-settings.sh
+
+# Or edit directly
+nano ~/.claude-mem/settings.json
+
+# View current settings
+curl http://localhost:37777/api/settings
 ```
 
-**Environment Variables:**
+**Advanced: Environment Variable Overrides**
 
-- `CLAUDE_MEM_MODEL` - AI model for processing (default: claude-haiku-4-5)
-- `CLAUDE_MEM_WORKER_PORT` - Worker port (default: 37777)
-- `CLAUDE_MEM_DATA_DIR` - Data directory override (dev only)
-- `CLAUDE_MEM_PYTHON_VERSION` - Python version for uvx/chroma-mcp (default: 3.13)
+For advanced users, settings can be temporarily overridden using environment variables:
+
+```bash
+CLAUDE_MEM_WORKER_PORT=38000 claude
+```
+
+**Note**: The settings file takes priority. Environment variables only apply when a setting is not present in the file.
 
 See [Configuration Guide](https://docs.claude-mem.ai/configuration) for details.