Normally, the content of files in the annex is prevented from being modified. (Unless your repository is using [[direct_mode]].) That's a good thing, because it might be the only copy, you wouldn't want to lose it in a fumblefingered mistake. # echo oops > my_cool_big_file bash: my_cool_big_file: Permission denied In order to modify a file, it should first be unlocked. # git annex unlock my_cool_big_file unlock my_cool_big_file (copying...) ok That replaces the symlink that normally points at its content with a copy of the content. You can then modify the file like any regular file. Because it is a regular file. (If you decide you don't need to modify the file after all, or want to discard modifications, just use `git annex lock`.) When you `git commit` it will notice that you are committing an unlocked file, add its new content to the annex, and a pointer to that content is what gets committed to git. # echo "now smaller, but even cooler" > my_cool_big_file # git commit my_cool_big_file -m "changed an annexed file" add my_cool_big_file ok [master 64cda67] changed an annexed file 1 files changed, 1 insertions(+), 1 deletions(-) For more details on working with unlocked files vs the regular locked files, see [[tips/unlocked_files]].