I want to fork both Twitter Bootstrap and one of its forks, Kickstrap. However, github thinks they're the same repo and after I fork one, Github shows the other as already forked to my account. Is it possible fork both to the same account?
(Use case is I need to add both as submodules to project, in which I'm scripting the generation of variations of a project starter template, some with Bootstrap and some with Kickstrap)
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Yes, you should use them as submodules and not fork them unless you want to contribute with them.
You cannot fork two repositories with the same name, that being the case of forks and original repos, as said here.
A work around would be, in case you want to contribute with both projects, to fork the most specific and latest one, in this case, Kickstrap.
This way, Kickstrap will point to the original root, being Bootstrap, and you can point your Pull Requests to either the original root or the final branch.
Kickstrap actually includes the full unmodified Bootstrap repo in Kickstrap/bootstrap/. This is by design so you can keep the Bootstrap core up-to-date without affecting your work in Kickstrap.
You could replace those contents with a git clone of bootstrap and just add Kickstrap/bootstrap to your .gitignore list so Xhibit doesn't tell you how he knows you like .git folders.