Revert "Avoid rebuilding everything due to submodule update."

This reverts commit 9fd24292c60c71824d9c5eda424efa4c73516a9d.
Revert "Auto-update submodules when building"

This reverts commit 6d4f765bc0b56bafd7132b3b9c384dd9dd8d4b4a.

I'm not smart enough to make it work for all edge cases this
early in the morning.

Sorry for the noise - if I try again, I'll make sure this actually
works before pushing to master...