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/shared/early-settings.ts

@@ -0,0 +1,31 @@
+import { join } from 'path';
+import { homedir } from 'os';
+import { existsSync, readFileSync } from 'fs';
+
+const SETTINGS_PATH = join(homedir(), '.claude-mem', 'settings.json');
+
+interface EarlySettings {
+  CLAUDE_MEM_DATA_DIR?: string;
+  CLAUDE_MEM_LOG_LEVEL?: string;
+  CLAUDE_MEM_PYTHON_VERSION?: string;
+  CLAUDE_CODE_PATH?: string;
+}
+
+/**
+ * Load settings for early-stage modules (paths, logger)
+ * Falls back to env vars, then defaults
+ */
+export function loadEarlySetting(key: keyof EarlySettings, defaultValue: string): string {
+  // Priority: settings.json > env var > default
+  try {
+    if (existsSync(SETTINGS_PATH)) {
+      const data = JSON.parse(readFileSync(SETTINGS_PATH, 'utf-8'));
+      const fileValue = data.env?.[key];
+      if (fileValue !== undefined) return fileValue;
+    }
+  } catch {
+    // Fail silently - fall through to env var
+  }
+
+  return process.env[key] || defaultValue;
+}