[server] move security/integrity hook management away from InternalSession.__init__ and to Repository.internal_{session,cnx} instead. Lets internal_cnx avoid deprecation warnings.

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