[ADAM-1342] Update CLI docs after #1288 merged.
[ADAM-1342] Update CLI docs after #1288 merged.

Resolves #1342. Adds validation stringency documentation for vcf2adam and
adam2vcf. Removes mention of the anno2adam and flatten commands, which were
removed in #1288.

heuermh/adam,heuermh/adam,laserson/adam,heuermh/adam,laserson/adam,massie/adam,bigdatagenomics/adam,bigdatagenomics/adam,bigdatagenomics/adam,massie/adam,laserson/adam,laserson/adam,bigdatagenomics/adam,massie/adam,heuermh/adam,massie/adam