You might be able to use diff/patch here, like we did in the olden days. They'll work on whole directory trees. But git is exactly built to solve this problem

You might be able to use diff/patch here, like we did in the olden days. They'll work on whole directory trees. But git is exactly built to solve this problem, and you should be able to do it without temporary parent directories. Why can't you check your work into a temporary branch on the server, push that branch up to a remote, and then check out that branch locally? Then do your work locally and/or remotely, and then push/pull/merge in all the places and life is good? All just using the existing git repo.