Funny story.
I had installed SublimeCodeIntel again to give it another shot and maybe I would like it. It managed to slow my computer down and I decided to delete it. So I opened my packages folder and deleted it. I continue along for a couple of days and Sublime was giving me weird errors in the status bar. It said things like “Couldn’t find language” so I figured their was something wrong with my tmLanguage file or something. I opened up my console and saw a bunch of references to codeintel. I thought to myself, “That’s weird. I deleted that a while ago.” So I went to my packages and there it is again. So again I deleted it. I relaunch ST and all is well. Then the errors start coming back. I look at my console and it says, “orphaned file found. Package Control reinstalling SublimeCodeIntel.” So as it turns out, I needed to uninstall SublimeCodeIntel via Package Control.
TL;DR Package Control will reinstall packages that were deleted manually from the packages folder.