Validate source compatibility before merging by position

[Duncan-JR]

MultiSourceView currently joins sources and ancestral annotations by position without checking contigs, REF alleles or duplicate annotation rows. This can select the wrong ancestral allele for the Unified Genealogies inputs (#1166).

For example, at GRCh37 20:10002611:

Input	REF	ALT	Ancestral allele
TGP and SGDP SNP	A	G	—
Ensembl deletion	ATTA	A	ATTA
Ensembl SNP	A	G	A

The lookup code currently selects the first Ensembl row, assigning ATTA to the SNP instead of A.

To prevent errors like this, I think we need the following:

1. Allow SNP filtering of the ancestral annotation input like with other sources, and reject remaining duplicate annotations at selected positions. This can follow the same filtering approach suggested in #1192.
2. Exclude sites with missing ancestral state (., N and empty strings) from both inference and augment_sites.
3. Check that selected records resolve to one shared contig name using each store's contig_id array. For example, TGP uses index 19 for 20; SGDP and Ensembl use index 0 for the same name. This requires fixing the bug in Fix minor inconsistency in ancestor inference algorithm #1194.
4. Check that REF agrees between sample sources and the selected annotations, raising an error with the source names and position on disagreement.

Together with inference-site filtering in #1198, these checks should make joining by position safe.