Include External is ignored

[joepio]

External resources are appearing in Collections with include_external set to false.

Relates to #316

[joepio]

Seems to be an issue with Db::tpf

[joepio]

Seems like QueryFilter does not use include_external. We could solve this in at least two ways:

Create a new QueryFilter with includes_external

This leads to an increase in indexed collections (more disk space used), and will make indexing slower.

Filter afterwards

Keep the indexed collections intact. Always pass include_external=true to tpf. This leads to some runtime overhead, although iterating over subjects should not be that expensive.