A while back I installed some Google software, I forget what it was, but it was something that attached itself to Google Chrome and was un-uninstallable short of uninstalling all of Chrome. It was a total pain in the a$$. Anyways, I was trying to put up a fight before going nuclear and just wiping Chrome, and during that fight, something went wrong (i.e., I didn't know what I was doing).

I remember messing around with the Applications folder somehow. I don't remember what exactly I did, but it perhaps involved some interchanging between the /Applications and /User/Username/Applications folders? Definitely some tampering in those areas, I'm sure at least about that.

Anyways, I've since updated and restarted my computer. Now, while all my apps work fine, many of them have blank icons - not on the Dock, those icons are fine, but in Spotlight search results, etc.

Currently, my /Applications folder contains only OS X-cooked-in applications. My ~/Applications folder contains cooked in apps AND post-OS/third-party apps.

There hasn't been any functionality deficit so far, but I don't like working on a machine where something isn't how it should be. I know my information was vague, but does anyone know what went wrong / how to fix it?

OS X Mavericks 10.9.3