There has been a feature added to make updates to ownlCoud so added apps will be maintained across versions. Add the following to your config.php:
array (
0 =>
array (
'path' => '/config/www/owncloud/apps',
'url' => '/apps',
'writable' => false,
),
1 =>
array (
'path' => '/config/www/owncloud/apps-external',
'url' => '/apps-external',
'writable' => true,
),
),
This will set up an /apps-external directory where your apps will be installed. This is where you would want to install any manually installed apps. When ownCloud updates, the standard ownCloud apps are installed in the /apps directory and the /apps-external apps are left alone.