I was testing the pdf submission plugin and then removed it and received a message that:

All data associated with the plugin 'PDF submission' has been deleted from the database. To prevent the plugin re-installing itself, you should now delete this directory from your server: /mod/assign/assignsubmission/pdf

The erroneous code is located in mod/assign/adminlib.php in the view_plugin_deleted function:

echo $OUTPUT->notification(get_string('plugindeletefiles', 'moodle', array('name'=>get_string('pluginname', $this->subtype . '_' . $plugin), 'directory'=>('/mod/assign/' . $this->subtype . '/'.$plugin))));

The assumption is that the subtype (assignsubmission) is going to be the directory path; however, the actual path is: mod/assign/submission/pdf.

Peace - Anthony