When I run git status, I have a bunch of lines of the form
deleted: dir/file.js
I can remove each of these individually wit
As rampion points out, you can still use git rm to stage the deletion of files that have already been deleted in your working copy (e.g. just git rm dir/file.js in your case.) If you have a lot of these files listed as "deleted:" under "Changed but not updated", I would first check that git ls-files --deleted produces a list of these files, and, if so, delete them with:
git ls-files --deleted -z | xargs -0 git rm