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Honestly a lot of searching.

The best tool for editing this game that I've found is Notepad++, specifically for the "Find in files" feature (hit ctrl-f, third tab). You can search all the scripts at once.

Start with the main variables file - it has most of these changes - /files/scripts/variables.gd

- That covers Pregnancy, selling, drop rates - lots of stuff.

Then if there's something you want to change that's NOT in variables.gd, use the search all files function to find it. Search the /files/scripts folder and you can make any of the other edits.  For instance, I like to make the wolf groups much larger - more fun, and helps me raise xp faster. I open /files/scripts/combat.gd and ctrl-f "wolf" and go through to figure out what needs to be changed.