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/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,