When updating hudson using the debian package, chmod is executed on the whole Hudson home directory, taking many minutes up to an hour if you have many jobs and builds stored.

This is the process that is executed:

chmod -R 750 /var/run/hudson /var/lib/hudson

Here's the pstree output, to see where it is executed from:

aptitude(31780)-+-dpkg(31855)---hudson.postinst(31887)---chmod(31975)