Hotfix 0.1.12
Pre-releaseHotfix. One thing is fixed, and it only concerns people who make or install mods. If you are on 0.1.11 and everything works, there is nothing here for you.
A mod can reach the disc archives now
Most of what is worth modding lives in the update archive, PATCH.DAT. Some things do not: the on-screen button prompts, for one, sit in GAME.DAT under GUI/FONT. A mod that named one of those never had a chance - the tool that injects the files was told where the update folder was and where the DLC packages were, and nothing else, so it could not find GAME.DAT, gave up on the whole mod, and left F4 -> Mods saying modcli failed, see the log. Mods touching PATCH worked, which made it look like the mod was at fault.
The game folder is searched too now. datfiles/GAME/... finds GAME.DAT, and so do GAME0..GAME4 and INSTALL0_*. Existing mods need no changes.
Reach for the disc copy only for something the update does not carry. If a file exists in both, the update's copy wins, so modding the disc copy of it changes nothing, PATCH is still where almost everything belongs.
DLC mods survive an install and an update
The installer applies mods at the end of a Russian install, and the updater re-applies whatever you had enabled after it patches. Both drive the same tool the F8 menu does, and neither told it where the DLC packages were. So a mod targeting a DLC archive, Super Sonic Infinite lives in DLC16, failed the install outright, and was quietly dropped on every update. Both pass the right folders now.
Also
docs/how-to-mod.mdnow says which archive to target and why the update usually wins.