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/main.go

@@ -118,12 +118,24 @@ var (
 	quietFlag      bool // Suppress non-essential output
 )
 
+// Command group IDs for help organization
+const (
+	GroupMaintenance  = "maintenance"
+	GroupIntegrations = "integrations"
+)
+
 func init() {
 	// Initialize viper configuration
 	if err := config.Initialize(); err != nil {
 		fmt.Fprintf(os.Stderr, "Warning: failed to initialize config: %v\n", err)
 	}
 
+	// Add command groups for organized help output
+	rootCmd.AddGroup(
+		&cobra.Group{ID: GroupMaintenance, Title: "Maintenance:"},
+		&cobra.Group{ID: GroupIntegrations, Title: "Integrations & Advanced:"},
+	)
+
 	// Register persistent flags
 	rootCmd.PersistentFlags().StringVar(&dbPath, "db", "", "Database path (default: auto-discover .beads/*.db)")
 	rootCmd.PersistentFlags().StringVar(&actor, "actor", "", "Actor name for audit trail (default: $BD_ACTOR or $USER)")
@@ -391,6 +403,11 @@ var rootCmd = &cobra.Command{
 			return
 		}
 
+		// Skip for root command with no subcommand (just shows help)
+		if cmd.Parent() == nil && cmdName == "bd" {
+			return
+		}
+
 		// Also skip for --version flag on root command (cmdName would be "bd")
 		if v, _ := cmd.Flags().GetBool("version"); v {
 			return