Revert "Don't create the $GIT_DIR/branches directory on init"

This reverts commit 0cc5691a8b05a7eabdeef520c94b1bb3bcac7874.

There is not enough justification for doing this.  We do not update
things in .git/branches and .git/remotes anymore, but still do read
information from there and will keep doing so.

Besides, this breaks quite a lot of tests in t55?? series.