refine: simplify node data JSON output

[joverlee521]

Discussed in Nextstrain meeting on 04 June 2026

There are extraneous fields in the node data JSON output of augur refine that are not normally used by downstream Augur commands. Removing these fields would simplify writing the branch lengths docs.

[jameshadfield]

In terms of what augur export v2 uses from a refine-JSON, divergence values are used here and temporal values used here and here. This would lead us to:

• Keep these values which are used for temporal trees: numdate, date_inferred (boolean), raw_date and num_date_confidence
• For divergence trees: keep one of mutation_length, branch_length, and drop the other
• Keep date (YYYY-MM-DD) even though augur export v2 doesn't use it
• Remove clock_length

For divergence trees it's been confusing to distinguish between subs/site & num. mutations. We could have augur refine use different keys (e.g. branch_length, num_mutations) for these metrics.