I am trying to add a branch to the master branch on GitHub and push a folder onto that branch.
The folder structure of the branch looks like - SocialApp/SourceCode/D
In my case, there was a .git folder in the subdirectory because I had previously initialized a git repo there. When I added the subdirectory it simply added it as a subproject without adding any of the contained files.
I solved the issue by removing the git repository from the subdirectory and then re-adding the folder.