Hey
I believe that MySQL/MariaDB* stores the database file on disk at var/lib/mysql
If you can copy the ITFlow www directory (be sure to include the .git hidden folder) and the database to a new system, presumably it's just like a migration. Then all you have to do is configure Apache & SSL.
I say presumably because I've never actually done this from the raw database files on Linux, but it's the same theory as mssql.
It's also worth noting your app version (the files) and database version should ideally match - i.e don't migrate the database but pull a fresh install, as the database schema may have changed.
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In terms of passwords, these are stored encrypted in the database using the master encryption key. To access these you'd need to either restore/migrate the ITFlow instance and login as normal or have access to the 'logins' table and the master encryption key to manually decrypt entries.
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I assume you've already read this but I'll link it anyway: https://docs.itflow.org/backups