Consumption of seqcol into existing file formats

Speaking in the VRC/VCF meeting, the consensus was these flat file consumers would work directly with the collection header format rather than working with seqcol serialised into their native header format. The thinking was there is no point spending time encoding to decode from one format to another. Much faster to just consume the native seqcol header and use that. Will mean a breaking change in the formats.

Start by reviewing the collection header format and the existing flat file consumers discussed in the issue. Read the VRC/VCF meeting context to determine which native seqcol header behavior is agreed, then document the required breaking changes and confirm that each affected format consumes the native header directly.

Written by the indexing model from the issue text.