Skip ModCandidates already considered in findModDirMods

Fixes issues with the coremods/mods folder merger causing coremods to be considered 'non-mod' files and added to the classpath.
Additionally fixes issues with the folder merge causing duplicate mods errors involving coremods and normal mods sharing a jar file.

This is an alternate solution to the same issue as #246, but it also fixes the issue mentioned there that that PR doesn't fix, that coremods (either skipped by that patch, or without any @Mod classes originally) are detected as non-mod files and re-added to the classpath.