Go into more detail on how you prepared Xcode for GitHub.
What you normally do to put an Xcode project on GitHub is to create a git repository for your project by choosing Source Control > New Git Repository and creating an external branch for GitHub from Xcode's source control navigator, which you can access by pressing Cmd-2.
When you put your project on GitHub like I described in the previous paragraph, you don't have to clone the project on GitHub.
It sounds like you have two versions of your project locally: the one you originally created and the one you cloned from GitHub. You have two options:
Work with the project you cloned from GitHub and stop using the one you originally created.
Place your original project on GitHub and stop using the cloned version.
The following article shows how to put a local Xcode project on GitHub:
swiftdevjournal.com/putting-your-xcode-project-on-github-bitbucket-or-gitlab/
Topic:
Developer Tools & Services
SubTopic:
Xcode
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