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/sync_test.go

@@ -441,7 +441,7 @@ func TestHasJSONLConflict_MultipleConflicts(t *testing.T) {
 func TestZFCSkipsExportAfterImport(t *testing.T) {
 	// Skip this test - it calls importFromJSONL which spawns bd import as subprocess,
 	// but os.Executable() returns the test binary during tests, not the bd binary.
-	// TODO: Refactor to use direct import logic instead of subprocess.
+	// TODO(bd-h048): Refactor to use direct import logic instead of subprocess.
 	t.Skip("Test requires subprocess spawning which doesn't work in test environment")
 	if testing.Short() {
 		t.Skip("Skipping test that spawns subprocess in short mode")