This is a test to see when the git hooks are overwritten by git-lfs. Note that pre-commit is a custom hook, and will not be overwritten by git-lfs.

This test was done on

 git-lfs/2.13.3
 git version 2.23.0

In order to track the changes to the git hooks, .git/hooks was changed to a symlink pointing to a folder in the repo (git-hooks). During setup, please run:

 rm -r .git/hooks
 ln -s ../git-hooks .git/hooks

The lfs filters were set to track the files with the extension .extension:

git lfs track '*.extension' 1>/dev/null

( please see .gitattributes)

The idea here is to demonstrate that the index is not updated:

touch data/file1.extension
git add .

# This will trigger git-lfs filter-process which tries to install the
# lfs hooks. It notices the hooks are identical, so it overwrites them.
# However, the git index is not updated with the new timestamp

git commit -m "Add a new file"

# The commit fails because the pre-hooks are checking against the old index

However, in some situations, git-lfs filter-process can be triggered by the refresh index operation itself [to be demonstrated]. Which ends up with an out-of-date index right after git update-index --refresh.