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This link suggests you could put rm ~/.bash_history in a script in /etc/X11/gdm/PostSession/Default.
Otherwise, changing /etc/init.d/rc.0 to include your rm command should execute it every shutdown (for every reboot, it'd have to be /etc/init.d/rc.6 I believe). See http://ubuntuforums.org/archive/index.php/t-256783.html for more info.
Take care with the last one - messing with the init scripts can lead to non-booting systems. I'd recommend making a backup of all the init.d directory before you do this!
That does not saving any history, even when the shell is active.
Hmmm... the history is kept in memory until you close the shell session. So the last N commands (depending on HISTSIZE) are available for the time the shell is active.
If I log into my server today, I can count on history tomorrow. Maybe the history is being held a different way, but I didn't add any programming to make that happen.
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