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)

cmd/bd/daemon_lifecycle.go

@@ -277,15 +277,15 @@ func stopDaemon(pidFile string) {
 		os.Exit(1)
 	}
 
-	for i := 0; i < 50; i++ {
-		time.Sleep(100 * time.Millisecond)
+	for i := 0; i < daemonShutdownAttempts; i++ {
+		time.Sleep(daemonShutdownPollInterval)
 		if isRunning, _ := isDaemonRunning(pidFile); !isRunning {
 			fmt.Println("Daemon stopped")
 			return
 		}
 	}
 
-	fmt.Fprintf(os.Stderr, "Warning: daemon did not stop after 5 seconds, forcing termination\n")
+	fmt.Fprintf(os.Stderr, "Warning: daemon did not stop after %v, forcing termination\n", daemonShutdownTimeout)
 
 	// Check one more time before killing the process to avoid a race.
 	if isRunning, _ := isDaemonRunning(pidFile); !isRunning {