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Description
This causes issues where if the MixinTweaker, a coremod, and a regular mod are in the same jar file, only the MixinTweaker and the coremod are loaded, but the regular mod is ignored.
As I mentioned here, this is due to the MixinTweaker removing the container file from the "loaded coremods" list, which forces FML to look through the container file again, but this only happens during the coremod discovery phase.
A solution as implemented here would be to also add the container file to the list of files that FML should reparse in the regular mod loading phase (usually, this is handled by FML here, but as the file is treated with tweaker handling processes, that code does not execute).
I will make a PR by the end of this week to resolve this issue, but if you want, feel free to take the linked code from FELaunchHandler. Note that those code makes some assumptions (for example, there is always a @mod in the same file), which should be catered to with proper checks.