In Painter I am never given an option to explore the cemetery. I have 7 perception, and no perception check ever even happens at the fountain.
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s stands for start, p starts for painter, r is for residential, t is for tavern, R is the ruined houses and above are in order the church and the cemetary.
You have to do things in order for the things to happen. Indeed, if you go to the church at the fountain before you talk to the painter there won't be any perception checks.
So, in summary, go to the painter, interact, ask about the old man and the young lady, go to the tavern, interact then threaten, go to the fountain, pass the check, go east, interact, look around, things will happen,
do not steal the painting,
go the church, interact, the priest will confess, then you can go to the cemetary and explore. Exactly as outlined in the guide. Then go to the paitner, interact, go to the ruins, confront the young lady, go to the painter again, interact and things will happen.