For example, consider the "Animator" character;

Several cards in this character read "Upgrade a card". These in-battle and permanent upgrade effects, while they work with the in-set infinite upgradables like Megumin and Entoma, they do not quite function well with the infinite Journal.

Other characters with a similar effect would have the same problem. E.g. custom Ironclad cards that upgrade cards. (Remember that Ironclad has Armaments), or relics that do the same (the Warped Tongs is a default relic that calls card.Upgrade).

It appears the Infinite Journal separately re-hard-codes a bunch of places in the default StS code where the Upgrade function is called. But what if a mod calls this function? Then things don't quite work out, hence some interactions just don't work correctly.

I'm not sure how to properly handle these cases to fix the issues, there's fundamentally a conflict. Perhaps some abstraction layer in BaseMod?