calendar: Close messages on clear

Currently the clear action in the section header simply removes all
messages from the section. While the result looks exactly as if the
close button of each individual message had been clicked, the messages
are not actually closed - after a restart (or some other condition that
triggers a reload), the messages simply reappear, which is confusing.
Do the expected thing instead, and make clear close all messages in the
section.

https://bugzilla.gnome.org/show_bug.cgi?id=746027