Introduction
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Inside the "Main Files" folder, you can find the romfs/a subdirectories. Inside these are a number of subfolders and files that correspond to different aspects of the game. If these files are present inside the mods folder created, then those changes should take effect ingame.

For a normal installation, you simply just use the entire contents of the "Main Files" folder.

However, if you don't want a particular set of changes for any reason, you can simply delete the corresponding file from your mods folder.

The files and what they change correspond as follows:

a/0/1/3 - Wild encounter data
a/0/3/6 - Trainer data
a/0/3/8 - Trainer Pokémon
a/0/7/3 - Text related to the gameplay (attacks, abilities etc)
a/0/8/1 - Text related to the story (NPC dialogues etc)
a/1/5/2 - Title screen (i.e. logo shown on the title screen)
a/1/8/9 - Move data
a/1/9/1 - Pokémon level up moves
a/1/9/2 - Evolution data
a/1/9/5 - Personal data (This is the Pokémon data for things like base stats, types, held items, abilities etc)
a/1/9/7 - Item data (This allows items like the Magmarizer to be used as an evolution stone, as well as containing item costs etc)

Alternative Files
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Additionally, inside the "Alternative Files" folder are alternative versions of the a/0/3/8 (Trainer Pokémon), a/1/9/1 (level up moves), a/1/9/2 (evolution data) and a/1/9/5 (Pokémon personal data) files.

You can replace the ones in the "Main Files" with these if you want a more vanilla experience (no ordinarily illegal moves, types etc) as they only contain the essential changes.

To do this, go into the respective subfolder (once copied into your mods folder) and replace the file with the alternative files equivalent.

For removing type and stat changes for example:
- Go into the romfs -> a -> 1 -> 9 folders, then delete the file called "5".
- Paste the "a195 Personal (Held item changes only)" file from the "Alternative Files" folder into the romfs/a/1/9 directory.
- Rename that "a195 Personal (Held item changes only)" to just "5" (with no file extensions).
- That's all there is to it!