As someone with quite a case of OCD, I don't like seeing resourcepacks appear in the packs menu in-game if they go unused. I have bubble popping being provided by another mod, so that feature is toggled off, and the pack remains deactivated. I decided to just delete them from within the jar, but doing so causes the game to crash on boot.

Latest: https://mclo.gs/mZRdv6l
Debug: https://mclo.gs/ww4gs8K
Crash: https://mclo.gs/zE2vWrE

Sorry, I'm not going to fix this. You shouldn't be deleting files from the jar. The whole reason it crashed is because the game is looking for files that don't exist. Subtle Effects isn't the only mod that adds built-in resource packs there are plenty of others. If it bugs you this much make a custom build of the mod for personal use without the resource pack registration code.