One thing I would like to point out: the plan was to have a layer of cilia as a shader placed over the cell membrane (a periphery organelle). The argument was that in real life, cells never have isolated patches of cilia, but coverings over their whole membrane:
I believe the current cilia-related code means cilia work as flagella do, i.e. a single hex of organelle. I'm not sure what the current consensus is, and I can't find the old discussion we had on it, so we might as well make that decision now.