How to install multiple modded clients on the same system

"What's the best way to install multiple Jedi Academy mods like JAEnhanced and TaystJK without them conflicting?"

We can think of OpenJK as the parent of both TaystJK and JAEnhanced. They are OpenJK, with changes. They don't need OpenJK present to exist standalone.

There's a few options as to how to install them together on the same system. In this guide I will present 3 options in order from best practice to worst practice.

Option 1. 

A single base folder with separate install folders for JAEnhanced and TaystJK. 

This option is the cleanest, but requires you to launch the game with a start-up script. If you don't mind writing/using a start up script, you can launch the game with start-up arguments to tell it where to look for the base assets, for example:

.
└── MyGames/
    ├── JediAcademy/
    │   └── base/ 			<- put pk3 mods you want globally here
    │       ├── assets0.pk3
    │       ├── assets1.pk3
    │       ├── assets2.pk3
    │       └── assets3.pk3
    ├── TaystJK/
    │   ├── taystjk/ 			<- put pk3 mods you want on TaystJK here
    │   │   └── japro-assets.pk3
    │   ├── taystjk.x86.exe
    │   └── run.bat
    └── JAEnhanced/
        ├── jaenhanced/ 		<- put pk3 mods you want on JAEnhanced here
        │   └── zZz_ja_enhanced.pk3
        ├── jaenhanced.x86.exe
        └── run.bat

To make TaystJK's run.bat, create a text file called run.txt, paste the following, and rename the file to run.bat, this file is your executable, you can right click it to create a shortcut, and place this shortcut where ever you like, you will use it to launch the game.

@echo off
start taystjk.x86 +set fs_cdPath "../JediAcademy"

And for JAEnhanced, simply substitute the .exe name.

@echo off
start jaenhanced.x86 +set fs_cdPath "../JediAcademy"

Option 2. 

Make a copy of base folder for each of TaystJK and JAEnhanced.

This option keeps everything self contained, but no there is no option of "global" pk3 mods without having a copy of the pk3 mod in each directory's respective base folder.

└── MyGames/
    ├── TaystJK/
    │   ├── base/ 			<- put pk3 mods you want globally here
    │   │   ├── assets0.pk3
    │   │   ├── assets1.pk3
    │   │   ├── assets2.pk3
    │   │   └── assets3.pk3
    │   ├── taystjk/ 			<- put pk3 mods you want on TaystJK here
    │   │   └── japro-assets.pk3
    │   └── taystjk.x86.exe
    └── JAEnhanced/
        ├── base/ 			<- put copies of pk3 mods you want globally here
        │   ├── assets0.pk3
        │   ├── assets1.pk3
        │   ├── assets2.pk3
        │   └── assets3.pk3
        ├── jaenhanced/ 		<- put pk3 mods you want on JAEnhanced here
        │   └── zZz_ja_enhanced.pk3
        └── jaenhanced.x86.exe

Option 3.
Install everything under the same folder.

There are reasons why this is a bad choice, for example, there are files that might be different between TaystJK and JAEnhanced, such as SDL2.dll and OpenAL32.dll which both launchers will try to share. Furthermore, if you were to try install 32-bit builds in the same folder as 64-bit builds, you will only be able to have one SDL2.dll present, and it only work on one of the two architectures, so the game will not launch on the other.

└── MyGames/
    └── JediAcademy/
        └── GameData/
            ├── base/ 			<- put pk3 mods you want globally here
            │   ├── assets0.pk3
            │   ├── assets1.pk3
            │   ├── assets2.pk3
            │   └── assets3.pk3
            ├── jaenhanced/ 		<- put pk3 mods you want on JAEnhanced here
            │   └── zZz_ja_enhanced.pk3
            ├── taystjk/ 		<- put pk3 mods you want on TaystJK here
            │   └── japro-assets.pk3
            ├── jaenhanced.x86.exe
            └── taystjk.x86.exe

Final Notes

In all options, you can put pk3 mods you only want to be active, on TaystJK for example, inside the taystjk/ folder, where you would already find japro-assets.pk3. That way nothing "installed to" TaystJK should conflict when the other launchers are used, regardless of where the base folder is.

In theory, TaystJK shouldn’t conflict with OpenJK or its derivatives, or the base game, if installed in the same folder (so Option 3 should work). I recommend Option 2 for users who don't want to involve a start up script, or Option 1 for those who don't mind a little bit more set-up. In these examples I have omitted the other files that come installed with both TaystJK, and JAEnhanced for clarity/brevity, you do need all of the supplied files.

I used TaystJK and JAEnhanced in this example, which are both forks of OpenJK. This guide is general and should apply for installing most other projects together. In this guide I also used Windows as an example. The .bat file examples will only work on Windows. They should be easy to re-write into a bash script or something compatible with other operating systems.