[pkg] Add missing entries to MANIFEST.in Detected by running `check-manifest <https://github.com/mgedmin/check-manifest>`_. Add a tox environment accordingly. Closes #15229018.

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