Template path registration in hook_civicrm_config breaks Joomla

When using a civix-generated extension, the include-path and template-path are modified by hook_civicrm_config. In Joomla, this hook may be called twice and break random bits (like the admin nav menu).

There's some discussion on irc between lcdweb and totten on 31-Jan-13 (circa noon Eastern time).

To reproduce:

• Install Civi 4.2.x and Joomla 2.5.x
• Setup Civi extensions
• Create a dummy extension with a dummy page (e.g. "civix generate:module" and then "civix generate:page") and enable it
• Log out
• Log in as admin
• Navigate to CiviCRM
• On first page load, the CiviCRM navigation renders as an empty black bar