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Atlan Mod Loader vs Eternal Mod Injector

Atlan's approach to mod-loading is fundamentally different from Eternal Mod Injector's. The major limitations of Eternal Mod Injector do not apply to Atlan.

Eternal Mod Injector Atlan Mod Loader
Replaces files inside of the vanilla game archives Builds it's own resource archive. The vanilla game archives are untouched
Modders had to know what archives contained which assets, and replicate this setup in their mods. Not an issue. The modded resource archive is loaded globally, so modded assets will always be loaded. 
Adding new assets to an archive, instead of replacing existing assets, could cause instability. Not an issue. Add as many new assets as you want!
Game updates frequently broke mods due to resource archive priorities changing. Not an issue. The modded resource archive will always have the highest priority.

Atlan does not make your mods immune to game updates. When a game update edits a vanilla file, you should update your mods to use that new version as a baseline. The dangers of outdated mod files vary based on their importance. Consequences can range from nothing happening, to core mechanics breaking, to your game crashing on startup.

What files are modified?

Atlan Mod Loader edits the following files:

The game executable file (i.e. DOOMTheDarkAges.exe)
base/packagemapspec.json
base/meta.resources
base/sound/soundbanks/pc/soundmetadata.bin
base/build-manifest.bin (DOOM: Eternal only)

The modded resource archive is base/modarchives/common_mod.resources

The modded StreamDB archive is base/modarchives/common_mod.streamdb

The modded audio archive is base/sound/soundbanks/pc/ATLANMOD.snd