Okay guys, I’ve cracked it!
The problem stems from the ignore file Unreal generates: it ignores a really important folder called the Binaries folder! So, for anyone who has this problem in the future, Here are the steps to successfully set up a repository:
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Create a folder for your repository.
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Inside the repository folder, create a new text document. Rename it .gitignore (ignore.conf for Plastic SCM). You may get a warning about changing file extensions. Ignore that warning.
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Inside the ignore file, paste the following:
.vs/* .idea/* .git/* .sln/* Build/* DerivedDataCache/* Intermediate/* Plugins/*/Intermediate/* Saved/*
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In the GitHub Desktop App, create a new repository. Give it the same name as the repository folder you created earlier, and set its path to the folder the repository folder is inside of.
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Publish the repository.
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Move the project files into the repository folder.
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Commit the changes.
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On the GitHub website, go into Settings>Collaborators and add any team members you need.
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Each team member will need to accept the invite. Then, on the Desktop app, they will hit File>Clone Repository. They can set whatever local path they want.