Define Jalview support for VCF with local contig sequence data

JAL-2738 and JAL-2743 cover loading VCF on to sequences where reference genome assembly coordinates are available (in Ensembl or EnsemblGenomes respectively).
VCF data may also use internal 'contig' references to sequences which are supplied locally in one or more Fasta files, e.g.
##contig=<ID=GL349624,length=2478080>
##contig=<ID=GL349625,length=1931609>
##contig=<ID=GL349626,length=1693096>
....etc...
where the contig ids e.g. GL349624 are the sequence ids in the Fasta file(s), and the first column of the VCF variant records ('#CHROM' location).

Need to understand workflows involving such data, and whether and where Jalview could add value.