update submodules when doing git fetch

[BenWibking]

This updates submodules with git submodule update --init after updating the git commit.

--init is required because there may be new submodules since the last checkout.

We need this for the Quokka GPU regression tests to work properly.

[zingale]

I think that this should be opt-in. For instance, with Castro, we can use submodules, but we don't for testing, so I don't want it to create submodules when testing.

[BenWibking]

I think that this should be opt-in. For instance, with Castro, we can use submodules, but we don't for testing, so I don't want it to create submodules when testing.

Ok, I've created a new option in the ini file for this. Let me know how it looks.