It's generally from researching a topic while working on a project. It's a bit like a cache of bookmarks, you don't really know what you're going to need until you've made some headway and found what was truly helpful that you may need later versus what you can safely close.
Anything that can work as well as Clearly. It's the best I've found at clipping articles for off-line archiving but it still makes me nervous having them on Evernote's platform when they said they were going to shut Clearly down (but apparently had a change of heart, for now).
It doesn't support a procedurally generated world like you are asking but there was a game for Sega CD called Third World War that I loved to play that had a good balance of diplomacy, trade, and war.
There's a Paradox game I played a few years ago called Supreme Ruler that I got excited about thinking it was similar but it tends to get bogged down in the military in my opinion.
Of course a friendly REPL is part of any good IDE, but I could not have learned Python as fast as I did without DreamPie[1]. It's basically an IDLE that separates the input from the output—color highlighted as well. It seems small, but at least for me it really made a big difference.