I'm having an issue in Eclipse in that my pull attempt fails, returning dirty worktree and naming a particular file. That's all fine and good--dealt with that in the past, but the issue this time is that the file is in a tree that I don't have in my local repo. How can I clean up the tree and complete the pull?
If you really have no work in progress, you can try the nuclear option of:
cd /path/to/your/local/repo
git reset --hard
That should reset your working tree to a clean state.
If that isn't working, re-cloning the all repo in another path, and re-importing it into Eclipse can help, as commented by the OP octopushugs.
I encountered the exact same problem shortly after my "fix." Luckily this time I had the offending worktree present in my workspace.
Deleting the offending file actually solved the issue and it was replaced in the pull.