You can use
$ git rm --cached ./whatever1.txt
after something is already under version control.
In fact, if you have "whatever1.txt" under version control and you want to remove it from git, but leave your working tree undisturbed, then just do this:
$ git rm --cached ./whatever1.txt
$ echo /whatever1.txt >> ${PROJECT_ROOT}/.gitignore
$ git status # this will now show ./whatever1 as "deleted" (from git, not your working tree, and will show gitignore as modified or created)
$ git commit -a
And that's it.
Only use
$ git rm
when you want to remove the file from both the working tree AND the git repo.
CAVEAT: The likely scenario you would use this is for removing IDE-specific files from git. In this example "whatever1" represents your IDE file(s) you're removing. If you are working on a project with several people and you push this changeset to a shared repo, then their "./whatever1" files WILL BE DELETED when they pull this changeset. The easy thing to do from here for the people on the receiving end is:
$ git checkout 1215ef -- ./file-you-want-to-restore ./another-file ./another-etc
(where 1215ef represents the last commit before the deletion)
This has the effect of restoring those files that were present at their last commit before the pull. After they have done this those files will be safe and not show up as uncommitted b/c they will fall under the exclusion of gitignore.
Good luck!