update changes.md and docs

Author: jameshadfield

CHANGES.md

@@ -11,11 +11,15 @@
 * Constrain `bcbio-gff` to >=0.7.0 and allow `Biopython` >=1.81 again. We had to introduce the `Biopython` constraint in v21.0.1 (see [#1152][]) due to `bcbio-gff` <0.7.0 relying on the removed `Biopython` feature `UnknownSeq`. [#1178][] (@corneliusroemer)
 * `augur.io.read_metadata` (used by export, filter, frequencies, refine, and traits): Previously, this used the Python parser engine for [`pandas.read_csv()`][]. Updated to use the C engine for faster reading of metadata. [#812][] (@victorlin)
 
+* clades, export v2: Clade labels + coloring keys are now definable via arguments to augur clades allowing pipelines to use multiple invocations of augur clades resulting in multiple sets of colors and branch labels. How labels are stored in the (intermediate) node-data JSON files has changed. This should be fully backwards compatible for pipelines using augur commands, however custom scripts may need updating. PR [#728][] (@jameshadfield)
+
+
 ### Bug fixes
 
 * filter, frequencies, refine, parse: Previously, ambiguous dates in the future had a limit of today's date imposed on the upper value but not the lower value. It is now imposed on the lower value as well. [#1171][] (@victorlin)
 * refine: `--year-bounds` was ignored in versions 9.0.0 through 20.0.0. It now works. [#1136][] (@victorlin)
 
+[#728]: https://github.com/nextstrain/augur/pull/728
 [#812]: https://github.com/nextstrain/augur/pull/812
 [#1136]: https://github.com/nextstrain/augur/issues/1136
 [#1152]: https://github.com/nextstrain/augur/pull/1152

docs/faq/clades.md

@@ -39,7 +39,7 @@ rule clades:
 As input, this command requires the tree, the output of the ancestral reconstruction steps and the translation step (assuming your clades are defined using translations), as well as the file with clade definitions.
 
 The output of this command is a json file in the common augur format that specifies `clade_membership` for each node in the tree.
-Nodes that didn't match any clade definition will be left `unassigned`.
-Internal nodes that form the root of clades will have an additional field `clade_annotation` that auspice uses to label branches in the tree.
+Nodes that didn't match any clade definition will be left unassigned.
+Internal nodes that form the root of each clade will also have a branch label assigned (you can prevent this by adding `--label-name none`).