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Under ubuntu 7.10, I have created a truecrypt volume in a file which I mount under ~/data and which holds my .mozilla-thunderbird, .ssh, .gnupg, etc. In my home directory I have created symbolic links to the .mozilla-thunderbird (etc) folders so everything "just works" after mounting the truecrypt volume.
My home directory is in a separate partition. If I forget to unmount the truecrypt volume before shutting down, on the next boot it complains that my home partition was not cleanly dismounted, and performs a filesystem check during boot. I can try to always remember that manual step during shutdown, but -- hey -- this is a computer! I want the machine to remember, because sometimes I don't.
I've created a truecrypt script in /etc/init.d and linked it as K02truecrypt in my /etc/rc* folders in an attempt to be sure the truecrypt volume gets dismounted. It works beautifully when I test it from a command line:
sudo /etc/init.d/truecrypt stop
results in "truecrypt -d" and the truecrypt volume is dismounted. But apparently during a shutdown, it does not dismount the truecrypt volume in time to allow the separate home volume to be dismounted, so I still
get the complaint on the next boot cycle about home not being cleanly dismounted.