Sync report says what stayed in the cloud, and notices branches checked out elsewhere

The end-of-turn directory sync report now has a keptInCloud section counting named, credentialNamed and dependencyRoots items, replacing a report that only covered nested repositories. Sync can also now refuse with checked_out_elsewhere, joining reasons like staged_changes, index_busy and ref_moved, with a new retry delay pair of 5s then 20s.