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I've finished cs50 and I'd like to save all code to my Github. Can I clone the submit50 repo which is private? I want to have all psets organized in folders in the master branch.

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You could clone the repo to from the command line, to your computer. Or, you can clone it within GitHub (if you're a free user you won't have private repos), using the Fork button.

The repository is organized in branches, not folders, one branch per submission (with the slug, for example cs50/2017/x/pset7, as its name). Maybe git worktree can be useful.

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