Alpha 6.6: --r[2]-[un]phased + "--allow-extra-chr 0"

This fixes a bug that occurred when --r[2]-[un]phased and "--allow-extra-chr 0" were used together.

This snapshot of the repo also includes a new vcf_subset utility for rapidly extracting a few columns from a very wide (possibly compressed) VCF, since plink2 --vcf is not designed for that use case.