Not sure if git got confused or I did something wrong. I had to do a clone of the repository after uploading some static libs. The libs are required as this was the distribution mechanism for the files. May have just been a one time thing but writing this down in case it happens again.
had to manually populate with the github web interface, couldn't use the github desktop. might have been a .gitignore setting that i just couldn't see the files, investigate later.