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/rename_prefix.go

@@ -22,7 +22,7 @@ import (
 
 var renamePrefixCmd = &cobra.Command{
 	Use:     "rename-prefix <new-prefix>",
-	GroupID: "advanced",
+	GroupID: GroupMaintenance,
 	Short:   "Rename the issue prefix for all issues in the database",
 	Long: `Rename the issue prefix for all issues in the database.
 This will update all issue IDs and all text references across all fields.