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/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)