git clone --mirror https://github.com/account/repo.git cloned-repo
cd cloned-repo
git push --mirror {URL of new (empty) repo}
# at this point only remote cloned-repo is correct, local has auto-generated repo structure with folders such as "branches" or "refs"
cd ..
rm -rf cloned-repo
git clone {URL of new (empty) repo}
# only now will you see the expected user-generated contents in local cloned-repo folder
# note: all non-master branches are avaialable, but git branch will not show them until you git checkout each of them
# to automatically checkout all remote branches use this loop:
for b in `git branch -r | grep -v -- '->'`; do git branch --track ${b##origin/} $b; done