title: Phusion Passenger: what causes "Cleaning stale instance...Directory not empty" message when using passenger-config or passenger-status
body: <p>It seems everytime I restart my Rails 6.0 application using <code>passenger-config restart-app /path/to/app</code>, I get a warning that there are stale instances, like so:</p>
  <pre><code>*** Cleaning stale instance directory /home/user/rails_apps/passenger-instreg/passenger.gJHicfi
      Warning: Directory not empty @ dir_s_rmdir - /home/user/rails_apps/passenger-instreg/passenger.gJHicfi
  </code></pre>
  <p>I did configure a specific <code>PassengerInstanceRegistryDir</code> in the Apache module configuration, as well as defined the <code>PASSENGER_INSTANCE_REGISTRY_DIR</code> env variable, but still, my <code>user</code> (under which I run the passenger utilities) does not seem have the correct permissions to remove the stale directories.</p>
  <p>How do I avoid this?</p>
  <p>I run Passenger 6.0.6 on Red Hat Enterprise Linux release 8.2 (Ootpa), with Ruby 2.7.1 installed via rbenv.</p>