Keep the metacoder taxonomy graph as one tree

[dsmutin]

Summary

• Metacoder heat trees and engine = "metacoder" differential trees were a forest: missing ranks became nodes named NA, and genus/species parsed from labels had one root per genus.
• Those nodes are now dropped and their children reattached, the same way metacoder::parse_phyloseq filters taxa named "NA". A root node is added only when the remaining ranks do not already share one parent.
• phyloseq_to_metacoder() uses that construction for archi_phyloseq lists, and parse_phyloseq for a real phyloseq object when that result is already one tree.
• The README heat tree is rendered again from the Kraken rank table, so the picture is one lineage under Bacteria.

Verification

• Genus and species Kraken taxmaps have one root (Bacteria), no nodes named NA, and every other node has exactly one parent
• A two-kingdom table and a label-only table each get a single root
• Harness visualization tests pass with metacoder installed