FLC OF A MLG TAXIED ACROSS A PARALLEL ACTIVE RWY CONTRARY TO ATC HOLD-SHORT INSTRUCTIONS CAUSING A GND CRITICAL CONFLICT WITH ANOTHER ACFT TAKING-OFF.

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AT THE SUGGESTION OF OUR RECURRENT TRAINING SCHOOL WE BEGAN A NEW PROC WHEREBY RIGHT AFTER TOUCHDOWN THE R SEAT (PNF) WOULD EXTEND THE AIR BRAKES -- EVEN THOUGH THE AUTO SYS HAS THEM DEPLOYED ALREADY. WHEN THE PNF PULLED THE HANDLE AS ABOVE WE RECEIVED A TKOF CONFIGN HORN WHICH COULD NOT BE SILENCED UNTIL CLR OF THE RWY BY RETRACTING THE FLAPS. WHILE THIS HORN WAS GOING OFF THE TWR OPERATOR TOLD US TO HOLD SHORT OF A PARALLEL RWY WHICH IS VERY CLOSE TO THE RWY WE HAD JUST CLRED. WE DIDN'T HEAR THE 'HOLD SHORT OF RWY 31L' BECAUSE OF THE HORN AND CHANGING TO GND CTL; BY WHICH TIME IT WAS TOO LATE. WE WERE ALREADY XING THE L RWY (31L) AND A SMALL CESSNA WAS TAKING OFF FROM AND IN FACT FLEW OVER OUR ACFT BY ABOUT 100 FT VERT. ALSO A PROB AT THIS ARPT (MDW) IS THE FACT THAT THIS RWY (31L) HAS NOT BEEN USED FOR A COUPLE OF YRS; ALL THE TIME I'VE GOTTEN USED TO XING IT WITHOUT PROB. I WAS AWARE THAT LATELY IT WAS BEING USED; BUT OLD HABIT PATTERNS ARE HARD TO BREAK. ESPECIALLY WITH A WARNING HORN GOING OFF IN YOUR EAR.