De-duplicate config fields after applying rules

[hinerm]

In 9ee3bbb I updated the plus function to distinct most lists.

However, this happens before applying conditional rules to the config, after which there may be more fields in need of de-duplication. We should check, in particular, if it's possible to end up with multiple JVM search locations.

Any fix may be appropriate for #39 as well

[ctrueden]

I took a quick peek, and see that the python and jvm root path logic each converts their respective directory list into a set via toSet() before scanning, so we're effectively already deduplicating those.