Adjust matching to be more consistent to Emperor/Empress

[fedarko]

See this thread -- basically, this would mean being more conservative about filtering stuff out of the table if it isn't already in the metadata (requiring the user to specify a --filter-missing-samples flag or something to do so). This would also apply for filtering out features in the table that aren't in the rankings (requiring the user to specify a --filter-missing-features flag or something).

We could either filter missing samples/features (as is done now) or assign it "placeholder" data. In the context of Qurro I think filtering makes more sense, hence naming these flags --filter-* instead of --ignore-*. But up to debate.

The current behavior in Qurro is just filtering the table and metadata as needed, while Emperor and Empress are somewhat more cautious.

This would technically be a backwards-incompatible change, so worth updating documentation / being careful to make the new UI intuitive for users.

Based on conversation with @ElDeveloper (thanks!)