I use git annex in direct mode and I have renamed a file. What should I do to make git annex understand that the file has just been renamed and not deleted/added?
The file I renamed is quite big and I would like to avoid having to copy it again to the remotes and I would also like to avoid having to redownload it again in all the repositories.
You don't have to do anything special, git-annex automatically detects when a file has been renamed.
Just
git annexadd the new file, and commit and sync like usual.