Easier way to manage multiple branches on GitHub?

I have a GitHub repository with two branches master and gh-pages. I am experiencing problems when switching between branches locally. Files and folders are not being copied correctly.

Is it possible to have each branch in a separate directory locally?

i.e.

/Users/macuser/github/my-ma开发者_如何学编程ster/
/Users/macuser/github/my-gh-pages/

instead of

/Users/macuser/github/my/

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Yes, there's no problem. Just git clone twice, then switch to the branch(es) you want. push and pull as needed.