Besides deleting(or re-locating) a whole bunch of unused .js files, the only real thing it seems we have to do is consolidate blocks/custom/arduino.js and blocks_compressed.js. When someone wishes to create a new block, it then simplifies things a whole bunch by them really only having to add onto adruino.js file for the block and then add a generator function for the other arduino.js file in generators. I think this is the right way to go about this, but please correct me if I'm missing something or if I misunderstood the assignment.
Running into a small bug presently with the consolidating (colors) attached below, but so far, everything else seems to be fine and compiling. I will take a look to address the bug later and also continue on getting to know ArduinoIDE for the purpose of our greater project.