Bugfixes:
- .map/.ped import now allows comment lines, as originally specified in the PLINK 1.0 documentation.
- "--export bgen-1.{2,3}" no longer generates an invalid .bgen when the sample-ID block must be omitted due to otherwise exceeding the size limit.
- BgzfFlush() and BgzfFlushTry() in include/plink2_bgzf.h should work properly again.
This also adds a warning when it looks like GATK GenotypeGVCFs needs to be rerun with --include-non-variant-sites, along with the --vcf-allow-no-nonvar flag to suppress it.