If I would want to back up my whole Linux system, what's unclear or maybe missing from Git Annex:

I'm not exactly sure about the best way to import the files. Should I just copy over all the files (e.g. using cp -ax /* ., or maybe rsync -a /* . or so) to the repo, and then use git annex add? (Let's skip /dev and maybe other special files for now.)

Let's say I added now all files to the annex.

I would also want to store the owning user, group, and access attributes, and maybe other extended attributes (ACL, xattr). This is not yet covered by Git Annex (by default), right? This could be stored as annex metadata. Or maybe better in some other way, because this would be per file path, and not per file content. Has anyone already done sth like this? It should not be too hard to do this, right?

I'm also not exactly sure how Git Annex handles symlinks. Would it store the original symlink? Or would it not handle them at all, and just add them to Git itself?

There will be some overlap of the files with other Git Annex repos (e.g. this could contain a subset of pictures I have elsewhere). I would want that the annexed data files are shared with my much bigger Annex repo which contains all my main data (pictures and lots of other stuff). This is actually the main reason why I consider using Git Annex as well for this purpose, and not some other solution, so that I don't need to store data separately, and get other benefits (to simplify my backups).