Background:

• I had Hudson installed from http://hudson-ci.org/debian.
• I upgraded Ubuntu from 10.04 LTS to 12.04 LTS.
• I installed Jenkins 1.424 from stock Ubuntu repos (and ended up with both Hudson and Jenkins installed side by side, which was kind of nice for a gradual migration)
• I moved all the jobs from Hudson to Jenkins manually, cleaning them up as I went, then shut down Hudson and disabled its startup script
• As time passed I kept making changes to Jenkins (new jobs, etc.)

Summary of the situation:

• a hudson package is still installed from the old hudson-ci repo
• jenkins and jenkins-common packages are installed from Ubuntu repos
• /var/lib/hudson exists with old configuration
• /var/lib/jenkins exists with new configuration
• /var/lib/jenkins is a mountpoint for an ext4 filesystem (/var was too small)

What I did next:

• added http://pkg.jenkins-ci.org/debian to apt sources
• tried to apt-get dist-upgrade to get the latest jenkins

What I expected:

• jenkins is upgraded and doesn't destroy my working configuration in /var/lib/jenkins

What actually happened:

• important configuration files like /var/lib/jenkins/config.xml and /var/lib/jenkins/.gitconfig were overwritten with stale copies from /var/lib/hudson

It's a good thing I had a backup!

There were other speedbumps along the road, and I'll file separate bugs for them:

• a conflict with a file from Ubuntu's jenkins-common, which I had to resolve by manually apt-get removing jenkins-common, after which I could run apt-get install jenkins again to continue the upgrade
• jenkins's post-install script failed with a bunch of errors like

mv: inter-device move failed: `/var/lib/hudson/jobs' to `/var/lib/jenkins/jobs'; unable to remove target: Is a directory

and to continue I had to mv /var/lib/hudson /var/lib/hudson.DO-NOT-TOUCH and run dpkg --configure --pending.