Currently, when installing an upgrade of civiCRM in Jooma! all of the menu items of type component which link to civicrm are set to deleted (published=-2) in the jos_menu table. THis means that each civicrm menu link needs to be recreated each time an upgrade is done.
Running the sql scrip belowt will restore the the menu items to published status, making it no longer necessary to recreate the menus manually.
/*This will take the menu links that were deleted as part of civicrm uninstall and restore them. */
/This assumes that prior to uninstalling civicrm you have trashed any deleted civicrm menus./
SET `published` =1
WHERE `link` LIKE CONVERT( _utf8 'index.php?option=com_civicrm'
USING latin1 )
AND `published` = -2
It would make joomla! upgrading that much less of a headache to include this either as a script or as part of the install script.