Certain aspects of Pixelmon, including special drops, NPCs, and structures, can be edited through JSON files. These files can be accessed by enabling their respective useExternalJSONFiles config setting(s) and then starting Minecraft, or restarting the server.
A while back I have started making a little program in "proceesing" for auto-converting MC models from JSON to source angine format. It actually worked, but more work was needed for automating texture conversion.
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