I am reporting this for the 1.12.2 game using Forge latest build (which is not available in the version dropdowns for this report). I have not tested with other versions. Minecraft Launcher updated a day ago and since then has broken our modpacks. The folder used for scripts, logs, the root folder, some binaries and some configs, has now swapped to be the .minecraft folder (or the app's installation folder if using the CurseForge launcher equivalent). These should all be referencing the installation domain folder for the modpack, not the root installation folder for the Launcher itself.

Implications are:
1) Clients on a multiplayer server no longer have access to scripts and some configs when they launch their games. This breaks crafttweaker especially but also some other mods which use folders stored on the modpack installation domain.
2) If a client (or single player user) places their scripts and other files into the .minecraft area so that the Launcher can read them, then all installations will read those scripts, causing modpacks to crash if a client has more than one modpack instance set up, as not all modpacks need the same files and folders.

You can replicate this behavior without mods simply by creating an Installtion with the Launcher and setting its domain folder to be somewhere other than the .minecraft root folder. Then observe that when you launch that installation the logs files are populated into .minecraft/logs and not domain/logs as expected. To replicate with a mod, try using a CraftTweaker script in the installation domain folder and observe that these scripts are not used by the game.