First off I want to say I fixed the problem before I had to post here. The reason I'm posting this is so anyone trying to find the answer on google can find this answer, seeing google was no help for me and I just made a good guess on how to fix it.
Now the issue was whenever I loaded Cydia, it would try to refresh but fail, wouldn't show any sources or installed files, couldn't search for anything, cydia was basically useless. Also I couldn't install deb files from ifile either. Command line in ssh was also messed up.
Also deleting the files in the list folder except for the partial folder didn't help me a single bit.
What I did to completely fix everything and not having to restore was just rejailbreaking using redsn0w. I checked all the options I had enabled using the latest redsn0w, loaded the default 4.1 iOS fle instead of my sn0wbreeze modded iOS file, and just let it rejailbreak. It instantly fix the problem. Do this at first if this happens to you and it should fix it right away and allow you to keep your phone as it is without having to reinstall everything.