Typing C-x C-q in an annexed file buffer causes Emacs to run "git annex edit". When the buffer is killed Emacs will run "git annex add && git commit -m Updated". Dired has been extended to not show Annex symlinks, but instead to color annexed files green (and preserve the "l" in the file modes). You have the following commands available in dired-mode on all marked files (or the current file): @ a Add file to Git annex @ e Edit an annexed file