File system permissions

Folder /tmp/magento found but not used in n98-magerun

The message indicates, that n98-magerun found a folder on your system which is usually used by Magento, if the configured var folder could not be accessed.

When n98-magerun executes certain commands, a Magento instance is initialized. But this instance uses another var folder, as indicated.

In that case, cache clearing might not have any effect on your website, as magerun is using a different folder.'));

If this is the case, make sure that your webserver can access the configured var folder.

How to check if there is really a problem

If you are on a developer system, just delete /tmp/magento, open your Magento website and see if the folder is created again. If the folder is created again, you have the problem.