refactor(doctor): consolidate maintenance commands + improve daemon startup

Consolidate clean, repair-deps, validate into bd doctor:
- Add validation checks to doctor (merge artifacts, orphaned deps, duplicates, test pollution, git conflicts)
- Add auto-fix for merge artifacts and orphaned dependencies
- Delete obsolete command files: clean.go, repair_deps.go, validate.go
- Delete orphaned test files: clean_security_test.go, validate_test.go

Improve daemon startup performance:
- Add fast-fail detection when daemon crashed (check lock before retrying)
- Reduce graceful shutdown timeout from 5s to 1s
- Skip daemon connection for root command (just shows help)
- Extract shutdown timeout as constants (daemonShutdownTimeout, daemonShutdownPollInterval)

Other changes:
- Move rename-prefix command to Maintenance group in help
- Fix Makefile to inject git commit hash via ldflags

New files:
- cmd/bd/doctor/validation.go (5 check functions)
- cmd/bd/doctor/fix/validation.go (2 fix functions)

internal/rpc/client.go

@@ -91,6 +91,16 @@ func TryConnectWithTimeout(socketPath string, dialTimeout time.Duration) (*Clien
 	if err != nil {
 		debug.Logf("failed to connect to RPC endpoint: %v", err)
 		rpcDebugLog("dial failed after %v: %v", dialDuration, err)
+
+		// Fast-fail: socket exists but dial failed - check if daemon actually alive
+		// If lock is not held, daemon crashed and left stale socket - clean up immediately
+		beadsDir := filepath.Dir(socketPath)
+		running, _ := lockfile.TryDaemonLock(beadsDir)
+		if !running {
+			rpcDebugLog("daemon not running (lock free) - cleaning up stale socket")
+			cleanupStaleDaemonArtifacts(beadsDir)
+			_ = os.Remove(socketPath) // Also remove stale socket
+		}
 		return nil, nil
 	}