This has been around in trunk and aurora builds for a few weeks already, but as a heads-up in case you haven't run into this yet: Applications are supposed to clean out any temporary files they've created when they are exiting, and there is a specific location (%TEMP% in Windows, usually C:\Users\...\AppData\Local\Temp; /tmp on Linux). Thunderbird is a bit too thorough and deletes all
files in the temp location on exiting, as long as it has operating-system permission to do so.
- Bug 1269878 - Thunderbird tries to delete user's temp directory upon exit
That's a nice recipe for problems if you run another application in parallel, the Thunderbird destroys its valuable data on the fly.