At the same time, OP seems a layman, and might be coming from things like Microsoft Word, where “Discard all changes” basically means “revert to last save”.
EDIT: After reading the related issues, OP may have also thought that “discard changes” was to uninitialise the repository, as opposed to wiping untracked files.
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.