Revert "Re-add header_mappings_dir"

This reverts commit 3bdcf29bf340659887d96e0f785dd5b364e43672.
Revert "Move libgit2 to the top level"

This reverts commit 0fc96d6eeccd5d4caf8f677e3d173ff800a2024f.
Revert "Remove header_mappings_dir so libgit2 headers are available"

This reverts commit 1966a5660fa2f03198556c46ba12748cd965339c.