I agree with you, in that it isn't the correct way to fix this. Since
you're editing a file provided for packaging, as opposed to upstream. I
also disagree with using `dirname $PIDFILE`, since the directory the pid
file is going to be stored in won't change often, if at all. Secondly,
don't use . as a separator for chown, use :

mkdir -p /var/run/popfile
chown -R popfile:popfile /var/run/popfile

Add that directly into the init script, and add a changelog entry.
Attach a debdiff to the bug, and I'll have a look at it.

In future, if you want a bug to be noticed, as opposed to by chance,
subscribe ubuntu-universe-sponsors.

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/var/run/popfile does not get re-created after reboot
https://bugs.launchpad.net/bugs/126894
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