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/reset.go

@@ -7,6 +7,7 @@ import (
 	"os/exec"
 	"path/filepath"
 	"strings"
+	"time"
 
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/git"
@@ -323,12 +324,12 @@ func stopDaemonQuiet(pidFile string) {
 
 	_ = sendStopSignal(process)
 
-	// Wait up to 5 seconds for daemon to stop
-	for i := 0; i < 50; i++ {
+	// Wait for daemon to stop gracefully
+	for i := 0; i < daemonShutdownAttempts; i++ {
+		time.Sleep(daemonShutdownPollInterval)
 		if isRunning, _ := isDaemonRunning(pidFile); !isRunning {
 			return
 		}
-		// Small sleep handled by the check
 	}
 
 	// Force kill if still running