Update documentation - testing/development

 * add sphinx_rtd_theme theme to dev requirements
 * change theme to sphinx_rtd_theme
 * fix section headers - use chapters where needed
 * refresh documentation where needed
 * add docs on development and testing

Closes #81 and #82
Remove incorrect comment

This comment is incorrect - we don't save config file anymore.
Completely remove comment as it's no needed - code is self explanatory.