The git solution for such scenarios is setting SKIP-WORKTREE BIT. Run only the following command:
git update-index --skip-worktree .classpath .gitignore
It is used when you want git to ignore changes of files that are already managed by git and exist on the index. This is a common use case for config files.
Running git rm --cached doesn't work for the scenario mentioned in the question. If I simplify the question, it says:
How to have
.classpathand.projecton the repo while each one can change it locally and git ignores this change?
As I commented under the accepted answer, the drawback of git rm --cached is that it causes a change in the index, so you need to commit the change and then push it to the remote repository. As a result, .classpath and .project won't be available on the repo while the PO wants them to be there so anyone that clones the repo for the first time, they can use it.
Based on git documentaion:
Skip-worktree bit can be defined in one (long) sentence: When reading an entry, if it is marked as skip-worktree, then Git pretends its working directory version is up to date and read the index version instead. Although this bit looks similar to assume-unchanged bit, its goal is different from assume-unchanged bit’s. Skip-worktree also takes precedence over assume-unchanged bit when both are set.
More details is available here.