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;
+}

src/shared/paths.ts

@@ -3,6 +3,7 @@ import { homedir } from 'os';
 import { existsSync, mkdirSync } from 'fs';
 import { execSync } from 'child_process';
 import { fileURLToPath } from 'url';
+import { loadEarlySetting } from './early-settings.js';
 
 // Get __dirname that works in both ESM (hooks) and CJS (worker) contexts
 function getDirname(): string {
@@ -22,7 +23,8 @@ const _dirname = getDirname();
  */
 
 // Base directories
-export const DATA_DIR = process.env.CLAUDE_MEM_DATA_DIR || join(homedir(), '.claude-mem');
+export const DATA_DIR = loadEarlySetting('CLAUDE_MEM_DATA_DIR', join(homedir(), '.claude-mem'));
+// Note: CLAUDE_CONFIG_DIR is a Claude Code setting, not claude-mem, so leave as env var
 export const CLAUDE_CONFIG_DIR = process.env.CLAUDE_CONFIG_DIR || join(homedir(), '.claude');
 
 // Data subdirectories