chore: Convert scattered TODOs to tracked issues (bd-lrj8)

Created 7 new beads to track TODOs that were previously inline comments:

- bd-7l27: Integrate migration detection into bd doctor (5 files)
- bd-6x6g: Add multi-repo target repo switching in bd create
- bd-ag35: Add daemon RPC endpoints for config and stale check
- bd-2dwo: Remove deprecated daemon logger function
- bd-0qx5: Implement Jira issue timestamp comparison for sync
- bd-7zka: Implement formula features (repeat, for_each, branch, gate, split)
- bd-h048: Refactor sync_test to use direct import logic

Updated 16 TODO comments to include bead ID references for tracking.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/create.go

@@ -161,7 +161,7 @@ var createCmd = &cobra.Command{
 			repoPath = routing.DetermineTargetRepo(routingConfig, userRole, ".")
 		}
 		
-		// TODO: Switch to target repo for multi-repo support
+		// TODO(bd-6x6g): Switch to target repo for multi-repo support
 		// For now, we just log the target repo in debug mode
 		if repoPath != "." {
 			debug.Logf("DEBUG: Target repo: %s\n", repoPath)
@@ -205,7 +205,7 @@ var createCmd = &cobra.Command{
 			// Get database prefix from config
 			var dbPrefix string
 			if daemonClient != nil {
-				// TODO: Add RPC method to get config in daemon mode
+				// TODO(bd-ag35): Add RPC method to get config in daemon mode
 				// For now, skip validation in daemon mode (needs RPC enhancement)
 			} else {
 				// Direct mode - check config

cmd/bd/daemon_logger.go

@@ -128,7 +128,7 @@ func setupDaemonLogger(logPath string, jsonFormat bool, level slog.Level) (*lumb
 }
 
 // setupDaemonLoggerLegacy is the old signature for backward compatibility during migration.
-// TODO: Remove this once all callers are updated to use the new signature.
+// TODO(bd-2dwo): Remove this once all callers are updated to use the new signature.
 func setupDaemonLoggerLegacy(logPath string) (*lumberjack.Logger, daemonLogger) {
 	return setupDaemonLogger(logPath, false, slog.LevelInfo)
 }

cmd/bd/jira.go

@@ -630,7 +630,7 @@ func detectJiraConflicts(ctx context.Context) ([]JiraConflict, error) {
 		// Check if updated since last sync
 		if issue.UpdatedAt.After(lastSync) {
 			// This is a potential conflict - for now, mark as conflict
-			// TODO: In a full implementation, we'd fetch the Jira issue and compare timestamps
+			// TODO(bd-0qx5): In a full implementation, we'd fetch the Jira issue and compare timestamps
 			conflicts = append(conflicts, JiraConflict{
 				IssueID:         issue.ID,
 				LocalUpdated:    issue.UpdatedAt,

cmd/bd/migrate.go

@@ -19,7 +19,7 @@ import (
 	_ "github.com/ncruces/go-sqlite3/embed"
 )
 
-// TODO: Consider integrating into 'bd doctor' migration detection
+// TODO(bd-7l27): Consider integrating into 'bd doctor' migration detection
 var migrateCmd = &cobra.Command{
 	Use:     "migrate",
 	GroupID: "maint",

cmd/bd/migrate_hash_ids.go

@@ -21,7 +21,7 @@ import (
 	"github.com/steveyegge/beads/internal/ui"
 )
 
-// TODO: Consider integrating into 'bd doctor' migration detection
+// TODO(bd-7l27): Consider integrating into 'bd doctor' migration detection
 var migrateHashIDsCmd = &cobra.Command{
 	Use:     "hash-ids",
 	Short:   "Migrate sequential IDs to hash-based IDs (legacy)",

cmd/bd/migrate_issues.go

@@ -12,7 +12,7 @@ import (
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 )
 
-// TODO: Consider integrating into 'bd doctor' migration detection
+// TODO(bd-7l27): Consider integrating into 'bd doctor' migration detection
 var migrateIssuesCmd = &cobra.Command{
 	Use:     "issues",
 	Short:   "Move issues between repositories",

cmd/bd/migrate_sync.go

@@ -13,7 +13,7 @@ import (
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
-// TODO: Consider integrating into 'bd doctor' migration detection
+// TODO(bd-7l27): Consider integrating into 'bd doctor' migration detection
 var migrateSyncCmd = &cobra.Command{
 	Use:     "sync <branch-name>",
 	Short:   "Migrate to sync.branch workflow for multi-clone setups",

cmd/bd/migrate_tombstones.go

@@ -69,7 +69,7 @@ func loadLegacyDeletionsCmd(path string) (map[string]legacyDeletionRecordCmd, []
 	return records, warnings, nil
 }
 
-// TODO: Consider integrating into 'bd doctor' migration detection
+// TODO(bd-7l27): Consider integrating into 'bd doctor' migration detection
 var migrateTombstonesCmd = &cobra.Command{
 	Use:     "tombstones",
 	Short:   "Convert deletions.jsonl entries to inline tombstones",

cmd/bd/mol_stale.go

@@ -64,7 +64,7 @@ func runMolStale(cmd *cobra.Command, args []string) {
 
 	if daemonClient != nil {
 		// For now, stale check requires direct store access
-		// TODO: Add RPC endpoint for stale check
+		// TODO(bd-ag35): Add RPC endpoint for stale check
 		fmt.Fprintf(os.Stderr, "Error: mol stale requires direct database access\n")
 		fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon mol stale\n")
 		os.Exit(1)

cmd/bd/sync_test.go

@@ -441,7 +441,7 @@ func TestHasJSONLConflict_MultipleConflicts(t *testing.T) {
 func TestZFCSkipsExportAfterImport(t *testing.T) {
 	// Skip this test - it calls importFromJSONL which spawns bd import as subprocess,
 	// but os.Executable() returns the test binary during tests, not the bd binary.
-	// TODO: Refactor to use direct import logic instead of subprocess.
+	// TODO(bd-h048): Refactor to use direct import logic instead of subprocess.
 	t.Skip("Test requires subprocess spawning which doesn't work in test environment")
 	if testing.Short() {
 		t.Skip("Skipping test that spawns subprocess in short mode")