So this all started because I didn't check the trash before emptying it. I was transferring a movie into the movies folder on my external drive using paste into folder, only for some reason, it sent the movies folder, along with 800 some odd films, into trash. I absentmindedly hit empty trash and a couple minutes after discovered what I had done. The drive is ntfs, so i was using ntfsundelete to recover, and it was working.
Until I discovered i had forgotten to tell it where to put the recovered files, so it put them in my home directory until the sd card was full. then it wouldn't let me delete anything so I was stuck. So I shutdown, pulled the sd card and removed some items by hand on another computer. I put my card back in the pi and booted it up and my custom login screen came up fine, but when i got into Mate, my custom background and icons were gone, and the top and bottom taskbars were too. SO I tried to change my background and it did nothing. Same with the theme. I've been using alt f2 to get to programs, and I know a few key shortcuts, but its a temporary fix.
Im curious what i did and how to get my system back to where it was.
Also, I use berryboot, not sure if that had something to do with it.
I'm running 16.04.2 on a Raspi3.