Impossible to link to the internal content

When manually entering link to the node it's in fact impossible to link to the internal site's content if the drupal is in the subdirectory.
May be, it would be good idea to process manually entered links with url() function? In this case:
1. The relative internal links would be converted to correct links automatically.
2. The URL aliases would be used automatically.

This functionality can be configured from the module's setup page.