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