refactor: make the graph the single source for tree output

[ivan-aksamentov]

refactor/graph-io-single-source -> fix/clock-negative-rate-warn

Resolve:

• kb/issues/M-io-tree-backed-output-order-inconsistent.md
• kb/issues/H-io-usher-ref-nuc-uses-parent-allele.md
• kb/issues/H-io-auspice-v2-required-updated-missing.md
• kb/issues/M-io-usher-mat-mutation-loss-is-implicit.md
• kb/issues/M-io-usher-zero-branch-length-collapsed.md
• kb/issues/N-io-tree-ir-architecture-unapproved.md

Update:

• kb/features/io.md: mark tree-output ordering, metadata, and reference-sequence parity

Create:

• kb/issues/M-io-usher-missing-branch-length-becomes-zero.md: record UShER absent branch length collapsing to zero
• kb/issues/N-mugration-confidence-rows-copied-for-output.md: record mugration confidence-row copy for output

Tree output was projected through an intermediate TreeIR layer built separately from the command graph. Direct formats (Newick, Nexus) consumed the ordered graph while TreeIR-backed formats (Auspice, PhyloXML, UShER MAT) projected the original graph, so the same output plan could carry different node orders, and the projection duplicated logic that drifted from the graph.

Make the graph authoritative for every writer [src]. Output topology order is applied once, in place, before any writer reads the graph, and each format adapter reads the command graph data directly instead of a projection. Auspice gains the updated metadata and root_sequence it was missing, and UShER export warns rather than fabricating a reference allele from a branch-local parent.

The single-source design removes the class of bugs where two representations of one tree disagree. Node ordering, mutation projection, and reference-sequence population now have exactly one producer, and the augur-facing formats match augur's node identity and ordering.

Work items

• Remove the TreeIR projection layer; format adapters read the command graph directly [src]
• Apply output topology order once before every tree writer [src]
• Introduce a unified Mutation/MutationEvent model for format projection [src]
• Warn on a fabricated UShER reference allele instead of emitting it