fix: Stale lock recovery and MCP init retry

Fixes #47 — "database is locked" after crash and MCP "not initialized"
when project IS initialized.

- FileLock: treat locks older than 10 minutes as stale regardless of PID
  status, covering cases where PID was reused or kill signal check fails
- MCP server: log errors from tryInitializeDefault() to stderr instead of
  silently swallowing, so transient open failures are diagnosable
- MCP server: retryInitIfNeeded() properly cleans up failed instances
  before retrying, preventing resource leaks
- CLI: add 'codegraph unlock' command for manual lock file removal

src/utils.ts

@@ -184,6 +184,9 @@ export class FileLock {
   private lockPath: string;
   private held = false;
 
+  /** Locks older than this are considered stale regardless of PID status */
+  private static readonly STALE_TIMEOUT_MS = 10 * 60 * 1000; // 10 minutes
+
   constructor(lockPath: string) {
     this.lockPath = lockPath;
   }
@@ -197,15 +200,18 @@ export class FileLock {
       try {
         const content = fs.readFileSync(this.lockPath, 'utf-8').trim();
         const pid = parseInt(content, 10);
+        const stat = fs.statSync(this.lockPath);
+        const lockAge = Date.now() - stat.mtimeMs;
 
-        if (!isNaN(pid) && this.isProcessAlive(pid)) {
+        // Treat locks older than the timeout as stale, regardless of PID
+        if (lockAge < FileLock.STALE_TIMEOUT_MS && !isNaN(pid) && this.isProcessAlive(pid)) {
           throw new Error(
             `CodeGraph database is locked by another process (PID ${pid}). ` +
-            `If this is stale, delete ${this.lockPath}`
+            `If this is stale, run 'codegraph unlock' or delete ${this.lockPath}`
           );
         }
 
-        // Stale lock - remove it
+        // Stale lock (dead process or timed out) - remove it
         fs.unlinkSync(this.lockPath);
       } catch (err) {
         if (err instanceof Error && err.message.includes('locked by another')) {
@@ -225,7 +231,7 @@ export class FileLock {
         // Race condition: another process grabbed the lock between our check and write
         throw new Error(
           'CodeGraph database is locked by another process. ' +
-          `If this is stale, delete ${this.lockPath}`
+          `If this is stale, run 'codegraph unlock' or delete ${this.lockPath}`
         );
       }
       throw err;