Starting with release 0.4.x you can add any and all POSIX compatible filesystems as a backup path in jotta-cli.
Using remote mounted filesystems, overlay filesystems or untested filesystems will cause jotta-cli to to display a warning:
$ jotta-cli add /path
Warning: The path you attempt to add is located on a remote mounted filesystem, overlay filesystem or untested filesystem. If the file system becomes unmounted or unavailable, jotta-cli might interpret that as the files and folders have been deleted, and thus the backed up files will be moved to the trash can on Jottacloud.
Do you still want to add the path to backup? (yes/no):
With this in mind, you should when possible not add any directories with mounts in them, but rather add the mount itself. The latter will log an error in jotta-cli status saying that the filesystems has suddenly gone, and server side data will not be deleted.
This feature has not been extensively tested, so please report any bugs to our bug tracker.