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Oh, and before trying fixes - make a backup of your precious files when booted in safe mode.
About that - I´d like to run a backup that takes all apps and their configuration files (more than my own docs and files, which I already have properly backed in Seafile). What would you recommend just for the apps, their configs (and maybe the repos) etc?
I think you're gonna find that a hard task. There isn't one universal directory where apps saves their configs and bin files. You'll find some in ~/.config