Restore from Disk

So the machine I have gitlab running on (along with a bunch of other things) has been vandalised or somehow corrupted. Permissions were changed and essential packages and configs were missing for essential parts of ubuntu. Im not sure what happened but recovery mode and several hours of diagnostics has lead me down a continuous path of fixing one thing, breaking another.

Fortunately it looks like gitlab files were untouched. But since its a hobby box I had never got around to checking how to properly make a backup. And now I can’t run the backup procedure from recovery mode either. I have access to the files on the disk but I’m not sure how I would go about restoring them to a fresh install of ubuntu/gitlab.