Add back all assemblies

[MillenniumFalconMechanic]

Add assemblies to assemblies.yml.
Make sure all ploidy is set for all organisms in organisms.yml

[NoopDog]

From Element

[NoopDog]

We will make ploidy multi-valued on organism.yml to not over-restrict the workflows when the ploidy can vary over the lifecycle or for other reasons.

#334