Can't update submodule commit using Github API

[jashandeep-sohi]

I'm using octopilot to update the commit that a submodule is at in the parent repo. This is done by using an exec updater and just running git commands manually to update the submodule commit, and then letting octopilot do the rest to create the commit. I know it's hacky, but it was working before #326.

The easiest fix for me would be to introduce a flag to force the commit to happen via pushChangesWithGit, but if you have better ideas, I'd be happy to implement that too.