For Citra:
All you need is a clean rom of Pokémon Omega Ruby or Pokémon Alpha Sapphire (1.0)
Right click Pokémon Omega Ruby or Alpha Sapphire (whichever game you're playing),
and click "Open Mods Location",
then place "RomFS" (from this folder) into that folder!
No patching required! Have fun!
Installing on a modded 3DS
Method 1 (patching with Luma):
Make sure "enable game patching" is enabled in Luma (you can check by holding
Select during launch to open Luma's config menu). If it's not, use the D-Pad to
select it and press A to enable it. Press Start to save your settings and reboot
the system.
With your 3DS's files open on your computer, place the "RomFS" folder into
/luma/titles/000400000011C400 (for Omega Ruby) or /luma/titles/000400000011C500
(for Alpha Sapphire)
Launch your game
Method #2 (recommended), 3dstoolkit
This method requires the use of another program, called 3dstoolkit, and a .cia of
OR/AS. The upside is that the game runs smoothly with no choppiness/slowness
whatsoever.
First up, make an empty folder; you can name it whatever (it doesn't really
matter).
Open 3dstoolkit, click the 'Extract' tab, and select your .cia of OR/AS as your
"source ROM". Select your output directory, and click "Extract" at the bottom. This
might take a minute or two.
Once that's done, download the files (the same version as the .cia, obviously) and
drag and drop the RomFS folder into your new folder, replacing any files with the
same name.
Using 3dstoolkit again, click the 'Build' tab, select the folder you extracted to
as the "Source Directory", and name the Output ROM whatever you want, but make sure
to save as a .cia.
Place your newly built .cia on your sd card, and install it to your 3DS using FBI.