The empty directories (`/var/run/shinken`, `/var/log/shinken`) are created at build time in `build_config.copy_objects_file()` of the `setup.py`. I can't figure why they are created at build time instead of install time though.

There are many empty dirs once the doc files are removed. Here is the full list:

* `/var/lib/shinken/doc`
* `/var/lib/shinken/doc/source`
* `/var/lib/shinken/doc/source/01_about`
* `/var/lib/shinken/doc/source/02_gettingstarted`
* `/var/lib/shinken/doc/source/02_gettingstarted/installations`
* `/var/lib/shinken/doc/source/03_configuringshinken`
* `/var/lib/shinken/doc/source/04_runningshinken`
* `/var/lib/shinken/doc/source/05_thebasics`
* `/var/lib/shinken/doc/source/06_medium`
* `/var/lib/shinken/doc/source/07_advancedtopics`
* `/var/lib/shinken/doc/source/08_configobjects`
* `/var/lib/shinken/doc/source/09_architecture`
* `/var/lib/shinken/doc/source/10_troubleshooting`
* `/var/lib/shinken/doc/source/11_integrationwithothersoftware`
* `/var/lib/shinken/doc/source/12_securityandperformancetuning`
* `/var/lib/shinken/doc/source/13_how_to_monitor`
* `/var/lib/shinken/doc/source/14_how_to_contribute`
* `/var/lib/shinken/doc/source/15_development`
* `/var/lib/shinken/doc/source/89_packages`
* `/var/lib/shinken/doc/source/89_packages/snmp`
* `/var/lib/shinken/doc/source/89_packages/webui`
* `/var/lib/shinken/doc/source/99_references`
* `/var/lib/shinken/doc/source/_static/images`
* `/var/lib/shinken/doc/source/_static/images/http/de3.php.net/images`
* `/var/lib/shinken/doc/source/_static/images/official/images`
* `/var/lib/shinken/doc/source/_static/images/official/images/callouts`
* `/var/lib/shinken/doc/theme/sphinx_rtd_theme`
* `/var/lib/shinken/doc/theme/sphinx_rtd_theme/static/css`
* `/var/lib/shinken/doc/theme/sphinx_rtd_theme/static/font`
* `/var/lib/shinken/doc/theme/sphinx_rtd_theme/static/js`
* `/var/lib/shinken/doc/tools`

Only these dirs are excluded by the above list comprehension, and they are related to doc.