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