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script_extenders
Due to the way ammo works, you can install just about any mod with it, even if the mod says it can't be installed with a mod organizer. This includes script extenders like skse, mods that typically go above the data folder like sse_engine_fixes, sseedit, etc. Since ammo isn't responsible for launching your game, you have to take these manual steps when using script extenders so steam will launch your game correctly. We'll use Skyrim Special Edition in this example.
- Download SKSE from https://skse.silverlock.org/
You must run the default SkyrimSELauncher.exe at least once before installing SKSE or you won't have proper files created like your inis. Just run the game normally through steam, proceed through the launcher, hit play, then exit the game at the main menu.
index | Download
-------|---------
[0] skse64_2_02_04.7z
index | Activated | Mod name
-------|-----------|------------
index | Activated | Plugin name
-------|-----------|------------
Skyrim Special Edition >_: install 0
index | Activated | Mod name
-------|-----------|------------
[0] [False] skse64_2_02_04
index | Activated | Plugin name
-------|-----------|------------
Skyrim Special Edition >_: activate mod 0
Skyrim Special Edition >*: commit
cd ~/.local/share/Steam/steamapps/common/Skyrim\ Special\ Edition
cp SkyrimSELauncher.exe SkyrimSELauncher.exe.bak
cd ~/.loal/share/Steam/steamapps/common/Skyrim\ Special\ Edition
cp skse64_loader.exe SkyrimSELauncher.exe
You can now launch skse through steam.
Note that any time you validate your game files, you will have to repeat copying skse64_loader.exe to SkyrimSELauncher.exe.
If you installed via the method outlined above, you can uninstall SKSE like this.
index | Activated | Mod name
-------|-----------|------------
[0] [True] skse64_2_02_04
index | Activated | Plugin name
-------|-----------|------------
Skyrim Special Edition >_: deactivate mod 0
Skyrim Special Edition >*: commit
If you ever want to uninstall SKSE, you can restore the original game launcher from the copy.
cd ~/.local/share/Steam/steamapps/common/Skyrim\ Special\ Edition
unlink SkyrimSELauncher.exe
mv SkyrimSELauncher.exe.bak SkyrimSELauncher.exe