Include all mutations in definition files?

[rambaut]

At the moment it is inconsistent whether the definition files contain all mutations from reference or just the ones on the stem branch. I.e., P323L, D614G etc. For simplicity and consistency, it may be good to include all of them. But the required number of 'alts' would need to be revised up.

[rmcolq]

We can make it more clear by putting some of them in a list in the JSON with key "ancestral" - this is what scorpio define already does when creating a new JSON file for a constellation if an outgroup is specified. The result would be that classify would use all the sites when classifying (so the rules should reflect that), but haplotype would only include the new sites.