Directories starting with .. -- only the top-level directory is scanned

Migrated issue

Reported by: jhodgdon

On api.drupal.org, the branches are set up with "files to parse" like this:
../src/drupal-6
rather than an absolute path like
/var/www/api.staging.drupal.org/src/drupal-6
or
/var/www/api.dev.drupal.org/src/drupal-6

This is apparently not working for parsing. The parser seems to have decided that there aren't any files to parse, or at least not very many.