Git update-index's assume-unstaged feature can be used to speed up git status and stuff by not statting the whole tree looking for changed files.

This feature works quite well with git-annex. Especially because git annex's files are immutable, so aren't going to change out from under it, this is a nice fit. If you have a very large tree and git status is annoyingly slow, you can turn it on:

git config core.ignoreStat true

When git mv and git rm are used, those changes do get noticed, even on assume-unchanged files. When new files are added, eg by git annex add, they are also noticed.

There are two gotchas. Both occur because git add does not stage assume-unchanged files.

1. When an annexed file is moved to a different directory, it updates the symlink, and runs git add on it. So the file will move, but the changed symlink will not be noticed by git and it will commit a dangling symlink.
2. When using git annex migrate, it changes the symlink and git adds it. Again this won't be committed.

These can be worked around by running git update-index --really-refresh after performing such operations. I hope that git add will be changed to stage changes to assume-unchanged files, which would remove this only complication. --Joey