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* pygit2: implement get/set/remove refs * pygit: implement iter_refs * pygit: implement resolve_rev * pygit2: implement working tree checkout * pygit2: implement reset, explicitly read/write index when used * pygit2: checkout does not need to reset index * pygit2: handle "-" branch shorthand in checkout * tests: install post-checkout hook should be run via gitpython * exp apply: use stricter exception handling for merge conflict * pygit: fix index read/write usage * gitpython: handle untracked file conflicts in stash apply * fix flaky/race index issue