If you clone a local git repository while you are on a given branch, also the new clone will be on that branch.
This is solvable by some easy git fetch but the HEAD will point to the first branch, and will give you headaches when you have to rebase.
the solution is *not* set-upstream, which will track changes from another remote by default, but *set-head* which will point to another local branch.
So, to restore sanity
git remote set-head origin master