Looking at my unpurchased upgrades in the Encyclopedia, the list appears to be wrong. I went to All and clicked "Hide upgrades you've purchased." Some of the items listed are ones I got for free and some are ones I have purchased.
Core Stats
Quoin Multiplier: maxed out
Intellectual
Transcendental Benefits II: have purchased, or at least not seen card in many moons
Perks
3 Jump cards: all purchased
3 Walk Speed cards: all purchased
Camera Mode, Encyclopeddling, Mappery, Skill Learning Brain, Snapshottery, Zoomability: grandfathered upgrades