Divergence (mutations) on the root node are ignored by augur export

[jameshadfield]

Current Behaviour
Datasets produced from augur export v2 require a divergence value to be set on the root node via a node-data JSON (under keys "mutation_length" or "branch_length") however the supplied divergence value is not used. All trees start with a divergence value of zero.

Expected behaviour
The provided divergence value at the root should be used.

(My understanding is that Newick trees can define divergence values ("length") for the root node, but if this is not the case then we should throw an error if the provided value is not zero.)

Possible solution
The best time to implement this may be in conjunction with #273 which will give augur export v2 the ability to read divergence from Newick trees.

The bug occurs because we initially call the recursive function convert_tree_to_json_structure using the default 3rd argument so that div=0 rather than using a provided root-node value (if provided).

Your environment: if running Nextstrain locally

• augur 12.0.0

Additional context
A related bug is that the root node must have "mutation_length" or "branch_length" as a key, else we don't set any divergence values in the resulting dataset.