Run script updates

[benj]

This ticket is for keeping track of desired changes/updates to the run scripts and/or run script generator. If you'd like an update please put it in this ticket so it doesn't get lost - update the list at the top and put a comment in.

Relevant files:

• generate_runscripts.py
• specim_qsub.py
• process_specim_line.py
• configSorter.py

Desired changes:

• Fix generate_runscripts.py to still generate an Eagle/Hawk config file with per-line information as far as possible even if not given a logsheet.
• Fix generate_runscripts.py so that it correctly takes into account the situation where the Eagle and Hawk file numbers are different.
• Rationalise the handling of the variables SORTIE and FLETTER - in some places they are confused and/or not as expected
• Improve configSorter.py so that it sorts entries into the same order that they're in the template file rather than alphabetically.