Finally got bored with the base game and tried out Codex. Let me just say I am impressed. And Thank You Ryika.
Although, I don't seem to be able to gain Affinity progress or building modules . After completing 3 building module factories the building module bar shows +3 per turn (should be plus +6 I believe) but the only building modules I have are from completed quests.

Also, I am showing +15 Purity progess per turn and after completing 3 Gene Gardens (which show that they add +10 per turn) the +15 is unchanged but my Purity Progress only advances after unlocking technology.

Thank You for any help, Im not sure if I've encountered a bug or if I'm not understanding the system correctly. I am new to the complex system of codex.