[pyramid] Avoid shutting down the repository at exit if it's already shutting down For install `cubicweb-ctl pyramid` command will explicitly call `repo.shutdown()` so the atexit hook is redundant. Prevent the latter to be executed when the repository is already shutting down (otherwise one gets an assertion error).

etc/init.d
etc/cubicweb.d
etc/bash_completion.d
usr/bin
usr/share/doc/cubicweb-ctl
var/log/cubicweb
var/lib/cubicweb/backup
var/lib/cubicweb/instances