Add convenience check for submodules

[jesse-lemurian]

A few people have accidentally cloned without --recursive . It would be pretty trivial to check if submodules are initialized and emit a specific error reminding them to initialize submodules

[EN1809]

I think I fixed this, but I'm struggling to check in the new hook. Probably something stupid on my end.

[scallyw4g]

I see you forked bonsai .. care to open a PR? @EN1809

[EN1809]

Done.