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)

Makefile

@@ -8,7 +8,7 @@ all: build
 # Build the bd binary
 build:
 	@echo "Building bd..."
-	go build -o bd ./cmd/bd
+	go build -ldflags="-X main.Build=$$(git rev-parse --short HEAD)" -o bd ./cmd/bd
 
 # Run all tests (skips known broken tests listed in .test-skip)
 test: