• a5.31 broke handling of contig names like 'chr1_KI270706_random'; this is now fixed.
• --chr-set's no-x, no-y, and no-xy modifiers would often just filter out variants on a forbidden chromosome; this has been fixed (i.e. PLINK 2 now consistently errors out).
• Command-line parser now enforces "must be used with --make-[b]pgen/--make-bed and no other non-merge commands" restriction on --set-hh-missing/--set-mixed-mt-missing .