The guide below was written by Jalathas.

You can see the properly formatted version here:
https://docs.google.com/document/d/10QIHDExHBHIzJRscP8Ph70Kn_0wUQT0q4aBni9vrh1E

Rising Ruby/Sinking Sapphire Decrypt9 Guide
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This guide is for creating a .cia file patched with the RR/SS files, for installation on a 3DS running custom firmware. For the purposes of this guide, Ill be assuming youre running Luma3DS, but any way you can launch Decrypt9 should work.
Things youll need
The latest release of Decrypt9 - https://github.com/d0k3/Decrypt9WIP/releases
The PackHack at this link - http://pastebin.com/A1s8cmsD
A .3ds rom of Omega Ruby or Alpha Sapphire, created with Uncart or similar (Name it something short with no spaces, like PKOR or PKAS.)
The RR/SS files - https://drive.google.com/drive/folders/0B-zmEVN0Mas6NTNyZkt2NE11bG8
Setting up
Before starting, we need to install the two tools you need for this process: Decrypt9 on your 3DS and the PackHack on your PC.

Extract the Decrypt9 download.
Copy Decrypt9WIP.bin to the /luma/payloads/ folder on your SD card.
Rename Decrypt9WIP.bin to x_Decrypt9WIP.bin, which will allow you to launch it by holding the X button while turning on the 3DS. If your X button is already assigned to another function, feel free to choose a different button.
Create folders named Decrypt9 and D9Game on the root of your SD card.
Extract the PackHack download.
Run SetupUS.exe to prepare the PackHack.
Patching the game
To patch the RR/SS files into the game, youll need to decrypt and unpack your OR or AS rom.

Place your .3ds file into the D9Game folder at the root of your SD card. 
Return the SD card to the console, if needed.
Holding X, turn on on your console. You should see a black screen with white text.
Choose Content Decryptor Options, then NCCH/NCSD File Options.
Select NCCH/NCSD Decryptor, and let it run to completion. This will take a long time, dont worry. A green message will tell you when the process is complete.
Hold left on the D-pad and press start to power down the console.
Return the SD card to the PC, if needed.
Move the .3ds file from your D9Game folder to the PackHack folder on the PC.
Run HackingToolkit3DS.exe.
Enter D to start the extraction process, then enter the filename when prompted. Again, the extraction will take some time, but at the end you should have several new folders including ExtractedRomFS and ExtractedExeFS.
Extract the RRSS download.
Navigate to the Rising Ruby Files or Sinking Sapphire Files folder, depending on the game youre modding.
Open the Drop-It-In folder.
Copy the contents of the romFS folder to your ExtractedRomFS folder, replacing any files if prompted. NOTE: If not using Luma3DS, do not copy DllField.cro. 
Copy the contents of the exe folder to your ExtractedExeFS folder, replacing any files if prompted.
Repacking your game and creating the .cia
With the files patched, we can now rebuild the .3ds file and convert it to a .cia file.

Run HackingToolkit3DS.exe.
Enter R to start the rebuild process, then enter the filename when prompted. As you might guess, this will take some time.
When finished, you will have a new .3ds file named <yourfilename>_Edited.
Move this new .3ds file to the D9Game folder on your SD card.
Return the SD card to the console, if needed.
Again, hold X while turning on your console to enter Decrypt9.
Choose Content Decryptor Options, then NCCH/NCSD File Options.
Select NCCH/NCSD Encryptor, and let it run to completion. You guessed it, itll take a long time. 
Once thats finished, select NCCH/NCSD to CIA Converter. Now you get to wait again. Last time, I promise.
Once the converter is done, your .cia file is ready to install through FBI or your other preferred .cia installation method.
Youre done! I hope this guide helped you enjoy Rising Ruby and Sinking Sapphire.
