Add bd doctor --fix flag to automatically repair issues (bd-ykd9)

Implements automatic fix capability for bd doctor with user confirmation
and security hardening.

Features:
- Organizes fix implementations under doctor/fix/ directory structure
- Shows all fixable issues and prompts for confirmation (Y/n) before applying
- Provides clear output about what was fixed and any errors encountered
- Re-runs diagnostics after fixes to show updated state
- Each fix is idempotent and safe to run multiple times

Automatic fixes implemented:
- Git hooks (runs bd hooks install)
- Daemon health issues (runs bd daemons killall)
- DB-JSONL sync problems (runs bd sync --import-only)
- File permissions (fixes .beads/ and database permissions)
- Database version mismatches (runs bd migrate)
- Schema compatibility issues (runs bd migrate)
- Gitignore updates (writes canonical template)

Security improvements:
- Prevents command injection by using os.Executable() instead of PATH lookup
- Prevents path traversal attacks with workspace validation
- Fixes race conditions by using cmd.Dir instead of os.Chdir()
- Corrects file permission logic (proper bit masking)
- Validates all operations run in beads workspaces only

Files changed:
- cmd/bd/doctor.go: Enhanced applyFixes() with confirmation and better UX
- cmd/bd/doctor/gitignore.go: Fixed permissions (0600 → 0644)
- cmd/bd/doctor/fix/common.go: Security helpers (getBdBinary, validateBeadsWorkspace)
- cmd/bd/doctor/fix/hooks.go: Git hooks fix
- cmd/bd/doctor/fix/daemon.go: Daemon health fix
- cmd/bd/doctor/fix/sync.go: DB-JSONL sync fix
- cmd/bd/doctor/fix/permissions.go: File permissions fix
- cmd/bd/doctor/fix/migrate.go: Database migration fixes

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

cmd/bd/doctor/gitignore.go

@@ -93,12 +93,11 @@ func CheckGitignore() DoctorCheck {
 // FixGitignore updates .beads/.gitignore to the current template
 func FixGitignore() error {
 	gitignorePath := filepath.Join(".beads", ".gitignore")
-	
-	// Write canonical template
-	// #nosec G306 -- 0600 is appropriate for gitignore
-	if err := os.WriteFile(gitignorePath, []byte(GitignoreTemplate), 0600); err != nil {
+
+	// Write canonical template with standard git file permissions (world-readable)
+	if err := os.WriteFile(gitignorePath, []byte(GitignoreTemplate), 0644); err != nil {
 		return err
 	}
-	
+
 	return nil
 }