Document reference and ancestral-allele requirements

[thierrygosselin]

ANGSD supports several likelihood, SAF and SFS workflows, but they do not all use the same allele convention or require the same external sequence.

This documentation clarifies:

• when -anc is required for polarized analyses;
• how -ref differs from an ancestral sequence;
• which SAF modes rely on inferred major/minor alleles;
• why precomputed VCF/BCF likelihoods still require compatible chromosome and allele labels;
• which parameters should be recorded for reproducibility.

No computational behavior is changed.

Related issues:

• realSFS saf2theta error: -> Pxroblem with size of dimension of prior 9 vs 44323 #637 — SAF/realSFS dimension mismatch and ancestral/reference assumptions
• -doSaf retains no site with -sites #385 — site filtering and SAF output inconsistencies
• folded SFS generated from only variant sites gives wrong number of individuals #321 — folded SFS interpretation when only variant sites are retained
• -doSaf produces unsorted positions and mixes up chromosomes #258 — chromosome ordering and reference-coordinate assumptions