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We need to bring the user instructions for webserver access up to date so that they match up with the new logic in apps_installer_has_write_access().
That being said... i think it would be great, for many reasons, to install apps in either sites/all/modules/apps or perhaps even a new sites/all/apps. The former being much easier and the latter being probably an interesting idea for the future. Stricter permissioning would be the main functional reason for both suggestions however i also think if we really want to push forward the idea of apps as being distinct from core/contrib and higher up in the stack then we might want to consider something like the latter.