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/doctor/fix/validation.go

@@ -0,0 +1,168 @@
+package fix
+
+import (
+	"bufio"
+	"database/sql"
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+
+	_ "github.com/ncruces/go-sqlite3/driver"
+	_ "github.com/ncruces/go-sqlite3/embed"
+)
+
+// MergeArtifacts removes temporary git merge files from .beads directory.
+func MergeArtifacts(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	beadsDir := filepath.Join(path, ".beads")
+
+	// Read patterns from .gitignore or use defaults
+	patterns, err := readMergeArtifactPatterns(beadsDir)
+	if err != nil {
+		patterns = []string{
+			"*.base.jsonl",
+			"*.left.jsonl",
+			"*.right.jsonl",
+			"*.meta.json",
+		}
+	}
+
+	// Find and delete matching files
+	var deleted int
+	var errors []string
+
+	for _, pattern := range patterns {
+		matches, err := filepath.Glob(filepath.Join(beadsDir, pattern))
+		if err != nil {
+			continue
+		}
+		for _, file := range matches {
+			if err := os.Remove(file); err != nil {
+				if !os.IsNotExist(err) {
+					errors = append(errors, fmt.Sprintf("%s: %v", filepath.Base(file), err))
+				}
+			} else {
+				deleted++
+				fmt.Printf("  Removed %s\n", filepath.Base(file))
+			}
+		}
+	}
+
+	if len(errors) > 0 {
+		return fmt.Errorf("failed to remove some files: %s", strings.Join(errors, "; "))
+	}
+
+	if deleted == 0 {
+		fmt.Println("  No merge artifacts to remove")
+	} else {
+		fmt.Printf("  Removed %d merge artifact(s)\n", deleted)
+	}
+
+	return nil
+}
+
+// readMergeArtifactPatterns reads patterns from .beads/.gitignore merge section
+func readMergeArtifactPatterns(beadsDir string) ([]string, error) {
+	gitignorePath := filepath.Join(beadsDir, ".gitignore")
+	file, err := os.Open(gitignorePath) // #nosec G304 - path constructed from beadsDir
+	if err != nil {
+		return nil, err
+	}
+	defer file.Close()
+
+	var patterns []string
+	inMergeSection := false
+	scanner := bufio.NewScanner(file)
+
+	for scanner.Scan() {
+		line := strings.TrimSpace(scanner.Text())
+
+		if strings.Contains(line, "Merge artifacts") {
+			inMergeSection = true
+			continue
+		}
+
+		if inMergeSection && strings.HasPrefix(line, "#") {
+			break
+		}
+
+		if inMergeSection && line != "" && !strings.HasPrefix(line, "#") && !strings.HasPrefix(line, "!") {
+			patterns = append(patterns, line)
+		}
+	}
+
+	return patterns, scanner.Err()
+}
+
+// OrphanedDependencies removes dependencies pointing to non-existent issues.
+func OrphanedDependencies(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	beadsDir := filepath.Join(path, ".beads")
+	dbPath := filepath.Join(beadsDir, "beads.db")
+
+	// Open database
+	db, err := openDB(dbPath)
+	if err != nil {
+		return fmt.Errorf("failed to open database: %w", err)
+	}
+	defer db.Close()
+
+	// Find orphaned dependencies
+	query := `
+		SELECT d.issue_id, d.depends_on_id
+		FROM dependencies d
+		LEFT JOIN issues i ON d.depends_on_id = i.id
+		WHERE i.id IS NULL
+	`
+	rows, err := db.Query(query)
+	if err != nil {
+		return fmt.Errorf("failed to query orphaned dependencies: %w", err)
+	}
+	defer rows.Close()
+
+	type orphan struct {
+		issueID     string
+		dependsOnID string
+	}
+	var orphans []orphan
+
+	for rows.Next() {
+		var o orphan
+		if err := rows.Scan(&o.issueID, &o.dependsOnID); err == nil {
+			orphans = append(orphans, o)
+		}
+	}
+
+	if len(orphans) == 0 {
+		fmt.Println("  No orphaned dependencies to fix")
+		return nil
+	}
+
+	// Delete orphaned dependencies
+	for _, o := range orphans {
+		_, err := db.Exec("DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?",
+			o.issueID, o.dependsOnID)
+		if err != nil {
+			fmt.Printf("  Warning: failed to remove %s→%s: %v\n", o.issueID, o.dependsOnID, err)
+		} else {
+			// Mark issue as dirty for export
+			_, _ = db.Exec("INSERT OR IGNORE INTO dirty_issues (issue_id) VALUES (?)", o.issueID)
+			fmt.Printf("  Removed orphaned dependency: %s→%s\n", o.issueID, o.dependsOnID)
+		}
+	}
+
+	fmt.Printf("  Fixed %d orphaned dependency reference(s)\n", len(orphans))
+	return nil
+}
+
+// openDB opens a SQLite database for read-write access
+func openDB(dbPath string) (*sql.DB, error) {
+	return sql.Open("sqlite3", dbPath)
+}