Whenever I try and clone any repository with something like the following command:

repo = pygit2.clone_repository(url="file:///srv/samba/files/programming/cli/modman-test", path="/tmp/modman")

The entire contents of the repo are staged for deletion.

I tried to get around this by passing 'checkout_branch="master"' to the clone_repository() function (as this fixes the issue just fine when I run 'git checkout master' from my shell), but that triggers a fatal error.