That’s now done, so once again everything but the Simulation Specifics section should be fully up to date.
I replaced the internal/external organelle system to one with three classes: internal, external and periphery. Internal and external organelles are placed in the same way (as hex arrangements, no more fiddling around with edges), but external organelles can have their orientation changed in the Appearance tab. Peripheral organelles were discussed here, and cover an entire cell with a shader coating. There are currently only three peripheral organelle types - cilia, lamellipodia and cell walls.
Reproductase is now gone everywhere but the Simulation Specifics section (which I’m yet to update). Hurrah! Instead, compounds are now converted to a locked-up mode, determined by how many organelles a cell has. These locked-up compounds can’t be accessed by any means except when a cell dies, when they’re distributed amongst floating organelles (which already contain the locked-up compounds used in the previous generation to produce them.