Luma LayeredFS doesn't look like it wants to patch updates, and from my experience OnionFS just immediately crashes even without any edits, so here's how to get them in another way!
Using command prompt is needed to do this, but lucky for you I've already written the commands.
- Extract your .cia file of the Minecraft Update (not regular Minecraft) from your 3DS, using any method. Make sure your extracted .cia is encrypted (you can encrypt it with Godmode9).
- Put this .cia in the same folder as the programs, and open HackingToolkit9DS.
- In HackingToolkit9DS, type CE and hit enter, then enter the name of your .cia file. Wait until it is done extracting.
- Rename the folder ExtractedRomFS to just 'romfs'. (Note: If this folder doesn't exist, then your .cia wasn't encrypted.) Make sure not to rename anything else!!
- Inside the romfs folder, make any edits you want to. There are other tutorials on making custom skins which you can follow.
Tip: The skin name can be changed in the .blang files in romfs\loc\
- Open command prompt in this folder by entering 'cmd' into the top bar of file explorer.
- In cmd, run this command: 3dstool -cvtf romfs romfs.bin --romfs-dir romfs/ and wait for it to finish building your romfs.bin file.
- Then run this command: 3dstool -cvtf cxi minecraft.cxi --header HeaderNCCH0.bin --exh DecryptedExHeader.bin --plain PlainRGN.bin --exefs DecryptedExeFS.bin --romfs romfs.bin and again wait until it is finished building your file.
- And finally, run this command: makerom -f cia -o newminecraft.cia -content minecraft.cxi:0:0 -ver 9408
(Note: 9408 is the version of the latest update, you can check your update version in FBI if you want to set it accurately.)
You'll get a warning running this command, but it's fine because the .cia functions just as it should anyway.
Simply just put this onto your SD card, boot up FBI, and install your .cia file!
Whenever you need to make an edit, just update the 'romfs' folder and run the 3 cmd commands again.