document reproducibility records for ANGSD analyses

[thierrygosselin]

For each analysis, retain the following alongside the output files:

• the complete command line and generated .args file;
• the ANGSD version, build date and HTSlib version;
• the BAM/VCF/BCF input list and reference and ancestral sequence identifiers;
• ploidy, genotype-likelihood and posterior-probability modes;
• site, depth, mapping-quality, base-quality and SNP filters;
• major/minor-allele and folded/unfolded SFS choices;
• random seed, thread count and any region or site-index files.

ANGSD defaults and output conventions can change between releases. A results file without this information is difficult to reproduce, even when the same nominal command is reused later.

Related to the reproducibility concerns raised across the SAF, SFS and BCF issues.