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/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)
 }