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/mol_current.go

@@ -209,7 +209,7 @@ func findInProgressMolecules(ctx context.Context, s storage.Storage, agent strin
 		}
 		resp, err := daemonClient.List(listArgs)
 		if err == nil {
-			json.Unmarshal(resp.Data, &inProgressIssues)
+			_ = json.Unmarshal(resp.Data, &inProgressIssues)
 		}
 	} else {
 		// Direct query - search for in_progress issues