This repair will leave the database in a still-broken state, but if this is run prior to purge-broken-files, less data will be lost.
Also updated the purge-broken-files operation to keep files and directories in the set, if they are only missing metadata.
This adds a number of additional features to the repair process so it can actually fully recover if all data is present.
Also added a several tests to ensure that the functionality works in multiple scenarios.
This fixes#5987
Carl Johnsen