Add a more exhaustive check for submodules

[player1537]

Right now we do a naive submodule check (if the directory exists, submodules have been pulled in), but we need a better one. When you clone (without --recursive), it still creates the directories, so the script incorrectly assumes they've been pulled in.

An easy fix might be to just always call git submodule update --init, but we'll have to check.