Phraseanet stores documents (images, audio, videos, pdf...) in the filesystem uses MySQL as database to store information, and relies on Elasticsearch indexes.
Backups should take care of those three synchronised elements, and also the application sources
These datas are saved in directories you probably defined during setup.
An incremental backup is recommended.
ApplicationBox and DataBoxes are MySQL databases related to a Phraseanet install.
Live backups should work.
Konsole Kommander has a command to backup your DBs:
php bin/console system:backup-db /path/to/DBBackupDirectory/
This command can be included in a backup script.
Applciation sources are genrally only modified when updating Phraseanet.
It can nevertheless be good to save at one time the sources after install and setup.
You may just save the config/ directory because everything you setup is stored in it.