Warning message seen when you upgrade logstash packages from 5.6.0 to 6.0Beta1

- Version: upgrade from 5.6.0 to 6.0.0Beta1
- Operating System: Ubuntu 64 bit
- Steps to Reproduce: When upgrading from 5.6.0 to 6.0.0 Beta1, noticed the following in the logs:

```
Preparing to unpack ./logstash-6.0.0-beta1.deb ...
Unpacking logstash (1:6.0.0~beta1-1) over (1:5.6.0-1) ...
dpkg: warning: unable to delete old directory '/usr/share/logstash/vendor/bundle/jruby/1.9/gems': Directory not empty
dpkg: warning: unable to delete old directory '/usr/share/logstash/vendor/bundle/jruby/1.9/specifications': Directory not empty
dpkg: warning: unable to delete old directory '/usr/share/logstash/vendor/bundle/jruby/1.9': Directory not empty
```
This is quite harmless, because it still allowed me to upgrade and I saw both the packages present in the directory. I think this is just a warning , but its definitely confusing to the users. Either way, it needs to be fixed.

cc / @LeeDr @jakelandis