Although now that I think about it, that could have been the intention here but not automatic, if that's why 5k+ files were staged without the user explicitly staging them. Extra tragic if that's the case.

From the git discussions around the issue, it wasn't that the files were automatically staged, but that the "discard all changes" feature invoked a git clean, and also deleted untracked files.

Since OP's project wasn't tracked, it got detonated.