Sorry but that doesn't really help, I do not have RPGMaker installed but do understand most of the human-readable code. I have found the external copy of FileGetter but you already said changing that doesn't actually do anything. Maybe I misunderstood you, I was under the impression the finished game was able to re-compile its assets from the raw JSON and .rb stuff without using the RPGMaker itself seeing as it still loads the .rb scripts from unpacked folders including modifications.
Then install it? It's not hard to find one in internet, provided that we discuss it on similar site.
It uses RGSS301.dll which is RPGMaker dll to repack (not recompile, but simply repack) it. Commands for it that are built in RGSS: save_data and load_data.
Whole repacking code is visible in FileGetter.rb, and you have said that you have seen it, so if you don't understand it, it's not up to me to tutor you. But there is
no more code that you didn't see in FileGetter.rb that does it, at all. Scripts.rvdata2 and some others are not being repacked by anything as it's RPGMaker default file.
If you want to change something in Scripts.rvdata2 you would have to get RPGMaker anyway or do a lot of manual parsing on its format using load_data and save_data that no sane person does.
Loading all .rb files is done from same FileGetter.rb, using simple load_script method, simply described as "read file and eval(...) it".
If you want to change FileGetter.rb behaviour, simply override its methods in a mod.
Load order described in Scripts.rvdata2 that is just few lines of code is: all base .rb files (if uncompressed, load all .rb from specific directories; if compressed, load needed rb file list from listX.rvdata2 which are generated by same FileGetter.rb, for order check FileGetter.rb), then load all mods from /ModScripts/, then load and execute Main.rb.
Loading of data is done in main (5_DataManager.rb to be precise) so you can mod FileGetter behavior using provided FileGetter.rb as reference.
