[10:08:41] [main/WARN] [FML]: Found FMLCorePluginContainsFMLMod marker in AppleCore-mc1.12.2-3.1.1.jar. This is not recommended, @Mods should be in a separate jar from the coremod.
[10:08:41] [main/WARN] [FML]: The coremod AppleCore (squeek.applecore.AppleCore) is not signed!

Forge 2702

Just confirming still a thing:

[17:02:57] [main/INFO] [FML]: Forge Mod Loader version 14.23.5.2855 for Minecraft 1.12.2 loading
[*snip*]
[17:02:57] [main/WARN] [FML]: Found FMLCorePluginContainsFMLMod marker in AppleCore-mc1.12.2-3.4.0.jar. This is not recommended, @Mods should be in a separate jar from the coremod.
[17:02:57] [main/WARN] [FML]: The coremod AppleCore (squeek.applecore.AppleCore) is not signed!

(I'm not suggesting it needs fixed; I'm actually confused why the first error exists given this IS a core mod! :)

AppleCore contains both a normal mod and a core mod in one jar. At some point, the Forge developers decided they wanted to discourage doing that for (what I'd argue are) dubious reasons.

Sounds reasonable though without knowing anything about the situation I couldn't say either way is better even if it sounds like there might be good reasons on both sides... I guess for bigger mods there might be better reason but there are good reasons against too... applecore clearly would be silly to split! (In my opinion ;)

Unfortunately, I don't really agree with the reasoning behind either of those warnings existing, so this is not likely to be fixed.