Firefox’s default total cookie protection is the real solution for this. Yes there is a facebook cookie on reddit, but it is sandboxed from the facebook cookie on cnn and the facebook cookie on youtube.
Also the noscript extension. It takes a while for you to curate your whitelists, but it is easy to do and nothings get to run without a active considerarion.

You want all applications to explisitly support each individual filesystem? That sounds insane. It is absolutly fair to demand some common ground like posix compliance. And a windows user can like anyone else just mount their git repo area using any other filesystem.

Absolutly. And they can just mount the git store using another filesystem. Would be the by far easiest solution.