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Fellowship of Scribes describes its effect as triggering "After playing an Action".  However, the option to spend a Favor to draw with Fellowship of Scribes occurs in between the play effects of Capital City - right before optionally discarding two cards for $2.  Example game Id: 97897178 (last decision as P2)

I have heard (but haven't substantiated) that there is a similar timing issue with Artificer.

I recently played a game with Governor and Inn.  On my turn, I played a Governor for remodel, my opponent upgraded into an Inn.  I got the option to shuffle cards from my discard into my deck (or at least, I had to click a button saying that I was done shuffling).