I booted up Linux Mint 12, logged in and was surprised by a few changes that suddenly appeared. I went to run Thunderbird only to find that the icon on the side panel (the one that appears when you trigger the upper left-hand corner) was missing. I typed in the program's name and it appeared. I click on it and it asked me to set up a mail account. I started up Firefox to find that my add-ons were gone. I opened up the file manager and my Home directory had many folders with random alpha-numeric names with the word "crypt" in them. Most of the expected folders in the directory were missing. When I clicked on one, I saw it was .thumbnails/normal. I logged out and logged back in and found those folders gone and the normal folder layout was restored. The problem is I now have duplicates of the same folders. Attached is a screenshot showing a Bash listing of the Home directory. These duplicates do not show up in Nautilus.
My theory is that when I executed Thunderbird, it didn't see the ".thunderbird" folder (which was present, but with a different name), so it produced a new one as though it were executing for the very first time. I believe the same occurred with Firefox.
Assuming my theory is correct, the solution would require that I delete the newer duplicate folders to restore the previous state. How can this be done?