.keep files are present to force git to track initially empty directories. Should the directories become populated the .keep file can be removed.
This is the GitHUB repo for the example nanoHUB app, "githubexample". The corresponding nanoFORGE wiki is: https://nanohub.org/tools/githubexample/wiki
This example was poorly set up because the GitHub repo and the tool have different names. Perhaps I have anothe example.