Update hierarchy to not depend on intermediate levels #251
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Resolves #246
This PR changes the hierarchy so that contained_by relations are defined between all levels, (phones are explicitly still contained by words even if syllables have been encoded) vs the assumption strict dominance (phones are contained by syllables which are contained by words, etc). This may have performance impacts, but does allow for future functionality with more arbitrary hierarchies, especially non-strict ones containing syllables and morphemes, or surface phones and underlying phones, etc.