Adds a check for checkpoints that take too long

Adds another hardcoded farm-specific setting for max checkpoint time per MB
and checks if a job that has gone over the run limit has had a checkpoint in
progress for longer than the maximum time (if so, it kills it).

Fixes a number of output message formatting issues.
Improves performance of jid file processing

Only processes jid file entries and bjobs -l parsing as far back
as is needed.
Improves handling of overtime-without-a-checkpoint

Also moves `bchkpnt` call into a subroutine
Adds warning message when bjobs -l fails