Modding
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Files in the patch directory override the files from the base game. This should work for all files in Audio, Graphics, Fonts and Data directories.

Scripts overriding works differently. You can add extra scripts, and override others, by adding them into patch/Mods directory (works exactly the same as the old Data/Mods folder, just in a different location). Only the individual functions and methods in the provided files override the base game, not entire files, and path name does not matter-- we encourage you to only override the functions you need. (There is no way to prevent loading of a base game script entirely.) 
NOTE: This does not apply to script files that end in text.rb-- for example, trainertext, montext, and ttypetext-- as well as townmap, mapconnections, bttrainers, btpokemon, and BossInfo. These must be overridden in the base game folders, not in patch, when used for compilation.

For example, patch/Graphics/Battlers/bulbasaur.png would take precedence over the normal Graphics/Battlers/bulbasaur.png.
However, patch/Mods/mycoolandawesomemod.rb would only override the specific functions, constants, and methods from the normal files present in the mod file. For example, if adjustBattleSpriteY is provided in mycoolandawesomemod.rb, it would override adjustBattleSpriteY from Sprite.rb.
You can use this for custom shinies or any other mods, instead of replacing the files in-game. 
Note that, for any non-script file, any file structure beyond the main directory (reborn folder / patch directory) has to be copied exactly, in addition to the file name, for the game to recognize your changes.

This should be the preferred way to install mods from now on. Do not replace base game files if you don't have to.
