I have working directory (#1) which has vendor directory(#2) in it. There is one dependency which I wanted to pull manually without composer (php version of npm/gem). I was working in #1, haven't saved/commited changes, when I decided I want to update library in #2. I navigated to vendor/myname, and did git pull repository.
Unfortunately it started to pull and merge to #1, instead of creating new directory in vendor folder.
Now I have:
git merge --abort might be what you're looking for.