Feature release

Feature release.

• Add seed_groups, replacing the previous include_samples option. It is a list of seed groups, each a list of strain IDs that are inserted into the ARG together as a single local tree. A tree is inferred over the group's haplotypes, the haplotype of the group's inferred ancestor is matched against the ARG, and the whole group is then attached at that placement. A group is inserted on the minimum date over its members, and members with later dates keep their real dates via negative ("in the future") node times. The previous include_samples formats (bare strain IDs, or (strain, match_date) tuples) are no longer supported.

• Fix retrospective matching on a day with no new samples. The table of samples already in the ARG was only rebuilt when there were samples to match, so on such a day the retrospective query ran against the previous day's table and could add a second copy of a sample that had just been inserted.

• Add basic support for non-SARS-CoV-2 genomes via an optional reference FASTA. Supply --reference to import-alignments and a reference_fasta key in the inference config; both default to the built-in SARS-CoV-2 reference, so existing workflows are unchanged. When reference_fasta is set, a reference_date config key is required (the date assigned to the reference). The redundant genbank_id reference-sequence metadata field has been dropped.