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Developer: Problems submitting project with sub-folders to GitHub

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We have followed the steps for submitting a keyboard to GitHub using the web interface, and are currently on this step: Step 3: Submitting a GitHub Pull Request.

We get to the Upload files step, and drag and drop the project folder, but it only submits the files in the top level folder, not the source sub-folder (and its sub-folders). I could probably create the source folder manually and add the files, but that would probably require committing changes more than once (committing for each folder separately). That doesn’t seem right.

Is there something we’re missing?

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