How do I set up PhpStorm for CiviCRM development?
Regarding your first question you can set up phpstorm to use another project directory rather than the .idea direcory in your civicrm root.

I usually have an install of Drupal with CiviCRM plus drupal modules plus extensions and only the extensions are link to git. 

I am also curious on how to use web tests in php storm... Did not know it was possible...