Move to latest libgit2 with PR #6706 merged

With libgit2/libgit2#6706 merged in we can now
use libgit2 from master. Small changes were needed.

This is needed in order to have stable hashes for e2e tests.

Previously we needed to use a patched version from:
https://github.com/u-quark/libgit2/commits/gg