A familiar story, the uploads directory was added to the Git repo and over time the client has made a number of edits which has removed some of these files which were being tracked by Git.
How can you remove them all quickly so that you can commit this change?
You can't delete the entire folder, there are files that need to be kept. You could use
git rm, but that would be time consuming to repeat for every single file.
Give this command a whirl, which will stage all deleted files ready for commit:
git ls-files --deleted | xargs git rm