feat: emit reconstructed ancestral sequences from timetree

[ivan-aksamentov]

Resolve:

• kb/issues/M-timetree-tip-state-flags-not-wired.md
• kb/issues/N-timetree-ancestral-sequences-output-unimplemented.md

Update:

• kb/features/timetree.md: mark the ancestral-sequence FASTA and the tip-state flags as implemented
• kb/issues/N-clock-unnamed-root-after-reroot.md: narrow the unnamed-rerooted-root defect to the clock command

Depends on: #938, #937

The timetree command accepted --include-leaves, --impute-missing-data, and the --reconstruct-tip-states alias but emitted no sequences, so the flags were inert and TreeTime v0's ancestral_sequences.fasta had no v1 counterpart under timetree.

timetree now writes a reconstructed nucleotide FASTA, selected with --output-reconstructed-nuc-fasta [src] and produced by default under --output-all [src]. It reuses the marginal reconstruction the ancestral command runs rather than a second sequence path: after the pipeline settles the tree, a refreshed marginal pass materializes each node's flag-aware sequence and emits it [src]. Rerooting leaves a fresh unnamed root, so every unnamed internal node is named once before serialization, matching v0 and the ancestral command across the FASTA, the augur node data, and the tree outputs [src]. The timetree step's produced-output set in the pipeline resolver gains the reconstructed FASTA so a later step can chain it [src].

Reusing the ancestral reconstruction keeps timetree sequence output on the same numerically validated path: internal-node sequences come from the marginal MAP states already used for the tree mutations, non-imputed tips echo their observed input exactly, and --impute-missing-data resolves ambiguous tip states to the marginal argmax as approved in the tip-reconstruction decision. Refreshing the marginal posteriors before reconstruction ties the emitted sequences to the final branch lengths, the same ordering the ancestral command uses.

Work items

• Add the reconstructed nucleotide FASTA to the timetree output surface, selectable and default under --output-all [src]
• Add the --output-reconstructed-nuc-fasta path flag to timetree [src]
• Emit the FASTA by reusing the ancestral marginal reconstruction, gated by the tip-state flags [src]
• Register the reconstructed FASTA in the timetree resolve_outputs mapping so the pipeline can chain it [src]
• Name the rerooted root before writing output so all timetree outputs carry NODE_<n> names [src]

Possible improvements

• Name the rerooted root in the clock command (kb/tickets/clock-unnamed-root-and-polytomy-nodes-after-reroot.md)