Patching .3ds files

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|	The end all be all of modifying 3ds rom dumps	|
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So you want to apply [insert romfs.bin/exefs.bin binary patch] or [insert romfs/exefs directory patch] like the FEF fan translation?
Well you've came to the right place, here well cover all the steps, from decrypting the .3ds file, to dumping the rom contents, to repacking as a 3ds and converting to cia.

As a side note the following method will strip the resulting .3ds file of the following.
FW and region info, effectively cryptofixing, this is not the same though as we arnt hexediting, its just the rom were compiling wont have any included on creation.
The manual
Download Play
Built in update files
Header
AP check
It also changes savedata to CARD2 instead of CARD1, i will not explain this difference so dont ask.

Now that that's out of the way you need some required software and homebrew.
https://github.com/d0k3/Decrypt9/releases
https://mega.nz/#!LlYEWCQD!VyS9XTuYfTPwLS4UG4CHDFEj33A3CU-NSSQL8Jovh6A

Decrypt9 goes into root:/3ds (if you dont know what root means stop here)
Packhack goes in where you keep your 3ds tools for pc.

First step, decrypting your rom.

1) Create folder root:/D9Game
2) Put the rom you want to decrypt into D9Game
3) Put your 3ds back together and start up homebrew menu
4) Launch Decrypt9 and select Game Options, then NCCH/NCSD Decryptor
5) Let it complete and then shut your 3ds off (its safe to pop your battery out for fast shut off, but make sure it says "Press b to go back or press start to reboot"
5) Put you sd card into your reader and go to the D9Game folder, at first it seems like nothing has changed when in reality the rom is now decrypted and we can dump the filesystem in folder format and bin format.
6) Put this .3ds file in the packhack folder and rename it gamenameabbrivatedDEC.3ds

Now for PackHack

1) Launch HackingToolkit
2) Enter "D" and press return
3) enter the full name of the decrypted rom
4) Y to decompressing code.bin

Now you have the laid out files of the rom, if you're using a loose file based patch (like the fef translation) you put the files in the "ExtractedRomFS/ExeFS" folders, if your using a romfs/exefs.bin based patch you apply the patch to the "DecryptedRomFS/ExeFS.bin"

Now to build the file into a .3ds

1) Once again open HackingToolkit
2) type 3DSB this will open another tool
3) Check use ExeFS binary unless your patch has files in ExtractedExeFS
4) Check Use RomFS binary unless your patch has files in ExtracterRomFS
5) Select open romfs and navigate to the romfs.bin file or the romfs folder depending on which you patched
6) Select open exefs and navigate to the exefs.bin file or the exefs folder depending on which you patched
7) Select open ExHeader and navigate to "DecryptedExHeader.bin)
8) Go to 3dsdb.com and look up the game your editing and find the correct region version and change CTR-P-XXXX to the proper serial listed on 3dsdb.com, for patches this will be change to CTR-U-XXXX the XXXX remains the same for updates and base games and usually for dlc as well (exception FEF) For example smash US would be CTR-P-AXCE, the publisher doesn't matter
9) Set save location to where ever with the name gameabrivatedPATCHED.3ds
10) Hit "Go"

Now you have a patched .3ds file containing not region info or fw info now to convert it to .3ds, for that follow my other guide for converting 3ds to cia.

http://pastebin.com/CeDh65is
with or without the spoof toggle the cia will work doesnt matter either way (for this case, making normal non patched 3ds files into .cia requires the fw spoof)