Git Sync weird behavior

I think I’m not getting something how this plugin works :confused:

After I set up, git is initialised in /user - .git and .gitignore are added. This already somehow messes up branch switching in PHP Storm. But that’s not all - in /user folder there are partial duplicates from root folder created too. Like /system, /tests and even /user itself. These folders contain only part of the original folders files.

What am I missing here? Why does it add these duplicates to /user?

BTW, at least for now I simply removed the plugin and all the trash it created, because I managed to get it working only in local, but not in prod (yes, I changed branch to main and also changed path to git). Also, as mentioned, I couldn’t work with PHP Storm, because it messed up all the branch switching (I was on myBranch, but IDE showed I was on main after I installed the plugin and I couldn’t checkout my real main branch or any other any more)