Update libgit2 to 3f8d005

Updating libgit2 to `0a62918`.  The current version in HEAD (`0383fa`) had an unfortunate bug updating the tree cache (https://github.com/libgit2/libgit2/issues/2629) that can cause some issues.
cf. https://github.com/libgit2/libgit2/pull/2644