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/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",