Hey guys. Shiny Quagsire finally got his archive_ncch merge to the Master Build which means, mods on an emulator!
So I'll be going to show you how to install mods on Citra Emulator. That way, it's easier to test model imports while your 3DS is being used or charged or don't have a 3DS(I'm looking at you Wii U Modders).

This guide will also help you install mods for Pokemon and other SaltySD supported games but use a different titleid. If you want to know the titleid of a specific game, go to 3dsdb.com. I might do a tutorial on installing Pokemon randomizers via SaltySD soon.

(Outdated Disclaimer)
Like from my last guide on installing mods,
If you're 3DS is not modded and below firmware 11.4, please follow this guide to install CFW on your 3DS. DO IT PROPERLY! If your 3DS is on 11.4 or above, you're screwed if you don't have flashcarts.
Come back here once you're done modding your 3DS.

(New Disclaimer)
Like from my last guide on installing mods,
If you're 3DS is not modded, please follow this guide to install CFW on your 3DS. DO IT PROPERLY!
Come back here once you're done modding your 3DS.

1. Requirements:

Modded 3DS with Luma CFW
Homebrew Launcher(for dumping NAND)
Super Smash Bros for Nintendo 3DS
Super Smash Bros for Nintendo 3DS Update 1.1.7 (Optional: DLC)
Smash 3DS dump(for obtaining decompressed code.bin)
A mod that you want to install
Citra 3DS Emulator

2. Preparation:

Installing Hacked 3DS and dump the game and update
Download the latest Nightly Build or Canary Build on Citra's website.

3. Dumping things from the 3DS:

Before you start playing the emulator, you have to dump these stuff. Sadly, I'm not allowed to share shared_font.bin, NAND, or game's update as it's considered warez and piracy. If I put these here, I might get banned from the site.
To dump shared_font.bin or other files from the 3DS, go to these 2 links. Here Here

If you don't know how to dump game and update from the 3DS, here it is:

3.1. Dumping Smash Bros digitally:

Open Godmode9(requires CFW) by holding the START button while booting
[A:]SYSNAND SD/title/00040000/000edf00/content/
Select 00000000.tmd
Look at the bottom screen and select TMD file options and Dump CXI/NDS file

3.2. Dumping Smash Bros physically:

Open GodMode9 by holding the START button while booting
[C:] GAMECART
Select 00040000000edf00.trim.3ds
Select NCSD image options and Decrypt file (0:/gm9/out)

3.3. Dumping game's update:

3.3.1. Method 1:

Open Godmode9 by holding the START button while booting
[A:]SYSNAND SD/title/0004000e/000edf00/content/
Select 00000005.tmd
Look at the bottom screen and select TMD file options and Dump CXI/NDS file

Once you're done dumping, insert your SD Card to your computer and you can get them on gm9/out folder.

3.3.2. Method 2:

Since Citra's latest update added Install CIA, you don't need to convert those to CXI.

Open Godmode9 by holding the START button while booting
[A:]SYSNAND SD/title/0004000e/000edf00/content/
Select 00000005.tmd
Look at the bottom screen and select TMD file options and Build CIA (standard) or Build CIA (legit)

Once you're done dumping, insert your SD Card to your computer and you can get them on gm9/out folder. For the update, place it somewhere on your Desktop. Proceed to Method 2.

4. HackingToolKit3DS:

Now that you got the game and update, use HackingToolKit 3DS to extract the game data. When the tool asked you to compress code.bin, type n.
Once the extraction is complete, go to ExtractedExeFS and get a copy of code.bin by CTRL + C it and then paste it on desktop.
Download HERE!

5. Patching code.bin:

I have been informed by one of Citra's contributors, Leo121, and he told me to take down the link to code.bin as it contains copyrighted materials. My apologies. If Shiny Quagsire add support to code.ips, it's fine to share those. To those who got the code.bin, you can still use it but you're not allowed to share it.
Follow this guide to get code.bin and patch it:
HERE

Another way to patch code.bin is to use LunarIPS. You have to download SaltySD’s code.ips and you need your decompressed code.bin and put them beside LunarIPS. The rest is self-explanatory. You also need to get the code.bin from the Smash 1.1.7 update. It’s in ExtractedExeFS.

6. Getting User Folder and Installing SaltySD:

So I'm gonna divide this into two, one is for the ZIP users and the other for the Installer users and each of them will divided into different methods. Sounds counfusing? This is ZIP users and this is Installer users:

ZIP:

Installer:

Let's start of with ZIP users because I don't like to install installers and some of the updates will break and have to wait for few days for a fix.

6.1. ZIP:

6.1.1. Method 1:

Open Citra Emulator and then close it.
Go to %appdata% and move Citra folder to the emulator folder and rename it to user.
Follow the guide on placing shared_font.bin and NAND(the 2 links before).
Place 00000000.cxi on user/sdmc/Nintendo 3DS/<zeros>/<zeros>/title/0004000e/content/
Rename it to 00000000.app(if asking, just click yes).
Move your code.bin to user/sdmc/Nintendo 3DS/<zeros>/<zeros>/title/0004000e/content/00000000.app.exefsdir/
Rename saltysd_code.bin to code.bin.

6.1.2. Method 2:

Open Citra Emulator and then close it.
Go to %appdata% and move Citra folder to the emulator folder and rename it to user.
Follow the guide on placing shared_font.bin and NAND(the 2 links before).
On Citra, go to File and click Install CIA
Locate your dumped CIA and install it. Wait until it's finish
Move your code.bin to user/sdmc/Nintendo 3DS/<zeros>/<zeros>/title/0004000e/content/00000000.app.exefsdir/
Rename saltysd_code.bin to code.bin.

6.2. Installer:

Go to %appdata% and open Citra folder
Follow the guide on placing shared_font.bin and NAND(the two links before)
On Citra, go to File and click Install CIA
Locate your .cia and install it. Wait until it’s done
Move your code.bin to Citra/sdmc/Nintendo 3DS/<32 zeros>/<32 zeros>/title/0004000e/000edf00/content/<name of the .app file>.app.exefsdir/

7. Installing Mods:

Well. Installing mods on an emulator is the same as installing mods on your 3DS.

Download a specific mod that you like here on Gamebanana(Wii U sounds would work for 3DS but you have to rename them), GBATemp(mainly this one and this one), or other sites.
If the mod contains a model folder or other folders, place them inside smash folder and you're done.
If the mod doesn't contains a model folder or something, create a new folder. Here are the directories for characters:Low Poly Models:saltysd\smash\model\fighter\<japanese names>\body\c0x <-- change x to 0-7
High Poly Models:saltysd\smash\model\fighter\<japanese names>\body\h0x <-- change x to 0-7
For musics and sounds, here's the directory:saltysd\smash\sound\bgm(background music), se(sound effects), vc(voice clips)
Open Smash 3DS and wait for it to load(some modpacks like UsM-eM, Neos, and Turbo'd will load too slow. That's normal)
Enjoy!

But since people have a hard time understanding things, here's an example.
I'll use N64 Mario as an example(this might get updated or trashed in the future).
If you look at the ZIP file, you can tell that it's not in its right folder which won't load the mod properly.

Fighter:
All you have to do is create a folder and name it model in smash folder.
Then, create another folder inside model folder and name it fighter.
Then, create another folder inside fighter folder and name it mario. (Case sensitive. No CAPS in the name)
Then, create another folder inside mario folder and name it body.
Lastly, drag c05 and h05 in the body folder.

UI:
All you have to do is create a folder and name it ui in smash folder.
Then, create another folder inside ui folder and name it replace.
Then, create another folder inside replace folder and name it chr.
Then, create five folders inside chr folder and name them:

chr_00
chr_20
stock_00
stock_90

Lastly, drag chr_00_Mario_06.tex to the chr_00 folder and vice versa.

Note: If you don't want to make folders, you could download the template.
https://mega.nz/#!lMpWzJoI!u8OPp0I3NxUpSfVOk71ae-J_6wN1Yjrg_0WBVBDqNi8

8. Reminder:

I've been using "000edf00" on this guide because my 3DS is US Region. If your 3DS isn't US, here are some other IDs.
EUR: 000ee000
JP: 000b8b00

9. Recap:

Citra Emulator
Dump shared_font.bin and NAND
Dump game and game's update
Move them to their respective folder
Install CIA on the emulator
SaltySD bin should be named code.bin
user/sdmc/Nintendo 3DS/<zeros>/<zeros>/title/0004000e/000edf00, 000ee000, 0000b8b00/content/00000000.app.exefsdir/
Game ID:

US: 00040000000EDF00
EUR: 00040000000EE000
JP: A0040000000B8B00

10. FAQ:

Q: Is this a legit emulator or is this a scam?
A: This is a legit 3DS Emulator on the works. Updates and archive_ncch are made by Shiny Quagsire. But Citra is made by bunnei and other contributors and devs.

Q: Can I play Citra Online with these mods.
A: Yes. Thanks to the devs for implementing Local Multiplayer Support back on November, you can fight with your friends or fight yourself. However, you cannot go to ONLINE cause it requires NNID and internet. As of now, you can fight with your friends at SMASH(or Local Play).

Q: Can I play it on mobile?
A: No. There's no existing mobile version. Other mobile versions that you saw on Youtube and Google are scams and probably uses Citra's name to get more attention.
However, they are in fact working on a mobile port with the help of SachinVin. But even with the android port, you can't play it with mods as they didn't implement the archive_ncch on mobile. Also, not many phones will work on this emulator at decent speed. I got mine booting the Homebrew Menu at 2FPS.

Q: The game lags so much.
A: It depens on the computer you're using. If you have a decent specs like I do, there will be some slow downs but some parts are full speed. There are custom or unofficial builds posted on GBATemp which gives you better performance. But however, some or most unofficial builds will run a certain game better than Smash. So I highly recommend you to try out the Canary Build.

Q: Does model imports and custom stages work on this emulator?
A: Yes.

Q: I can't load Turbo'd, Neos, and USM-eM on this emulator.
A: Just like the 3DS, modpacks will load slow at start. Just wait for few minutes.

Q: Can I use this emulator to test mods like model imports or texture hacks?
A: Yes. You can use the emulator for testing purposes. It's easier to test on an emulator than reinsert your SD Card/Micro SD Card a dozen times.

Q: When I tried to update, I got this error "The file that you are trying to install must be decrypted before being used with Citra. A real 3DS is required". Send help.
A: That's because you illegally download that! No piracy and no, I'm not allowed to send you the .cia. Don't even DM me too. Either get a 3DS and dump it yourself or screw it and leave.

Q: I download a mod and it doesn't work!
A: There are alot of reasons why it doesn't work. Most notably, you didn't install the mod right as some mods don't have the right directory or missing a folder. Others have the folder with captial word like Smash or Luigi. Files are case sensitive. Some folders have to be lowercase.

Q: Will this work on older versions like 1.1.4 or 1.0.0?
A: No. SaltySD only support the latest version.

Q: How can I make the Wolf mod work? When I try to side b, he doesn't go up but go straight.
A: Probably you download an old code.bin patch and use it. Anything that is 2-3 years old code.bin you might found online will not make this mod work. You get a decompress code.bin from the 1.1.7 update and code.ips from SaltySD and patch them with LunarIPS and done.

There are plenty of questions asked. I'll update once you've got a problem or I made an error on the guide. Anyways, enjoy using them and record high quality for some Smash bros Youtuber who showcase salty videos.

Other questions will be in the other guide right HERE!

11. Video:

If any concerns, visit the Smash 3DS Hacking Server.
Also, I got DM from someone for asking where the Discord server is. So for both PC and mobile users, here's where you can find the Discord server:
PC: