Ah. What you are saying is that a README in the root directory will show up on the project page. Did not know anything about that. The solution is obvious -- I'll get to that in paragraph three.
Please consider that if you want to share this though the KoLmafia script manager I am disinclined to add anything that is on GitHub. Anything in the next paragraph will be irrelevant if you take this advice, but...
You can put your README in the base directory along with a directory called /MyScript (or whatever name you like). Put dependancies.txt in /MyScript and the other files in subdirectories of /MyScript. Then when you add that script to KoLmafia, just do it with /MyScript as the base directory. Mafia need not even know that there is a root directory.