If starting crystal-facet-uml from command line, there are a couple of options, call crystal-facet-uml -h for a list.
To run consistency checks, use the -t option:
crystal-facet-uml -t my_database_file.cfu1 || echo "ERROR $?"
To repair the database, use the -r option.
To store a database in a version control system (vcs) like svn or git, store the json file format *.cfuJ to your vcs.
Note that this feature requires at least version 1.35.0, better version 1.39.0 to work smoothly.
Do not synchronize the file with your vcs while you modify it at the same time; save your changes first and re-open the json file afterwards.
In case of merge conflicts in *.cfuJ files, note that uuid strings do uniquely identify all json objects. Relations between objects are defined by these uuid strings. In contrast to uuids, integer-id can be changed as long as they are unique among all objects of same type within the file.