Bugfix: Handled edge case where runs could become stuck if FTP goes down...

Bugfix: Handled edge case where runs could become stuck if FTP goes down before the time at which warnings start to be issued. Bugfix: Corrected calculation of data availability/warning times. Added more structure to the inProgressFile handling. TODO: Deal with TZ/UTC offset around midnight causing spurious warnings. TODO: Check warning emails are always successfully sent