Having in mind the shared details, I suppose the changes are not actually committed. Would you please check if you have committed the new folders and files?
To check that in the top menu bar, click Version Control → Commit. In case you can see the newly added files and folders in the list, this means they are not committed and will not be pushed to the remote repository. Please note t
he "configure remote repo" wizard just pushes what is already committed and it is not expected to commit any local changes i.e. if you have local changes they will not be pushed but kept locally.
To resolve it, I suggest you to try committing your changes and then request a push again. More information about the process could be found here
Let me know if this helps.
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