Do not want to check if last argument is a flag.

If the last option is a flag then we would try and access the element
beyond the end of the array as the filename and cause a crash.
Refactor the reading of the option file.
Attempt to future proof commands line options, pedantic console output formatting.
Future proof the range of N and Z

The 'current' max values of N and Z were used throughout
the code. Create a #define so that the discovery of a new
nuclues requires a single change rather than a grep discovery.
Use a more sensible variable name.
Lets use ***=ERROR and **=WARNING when printing to screen.
The output filename was being constructed twice if it was specified. Other minor print to screen tweaks.
Introduced a bug in commit d1015061. Loop limit didn't vary with actual number of arguments.
More playing with the construction of the output filename.

Cannot see a way to generalise for all permutations of inputs so
do it differently depending if 0 or >0 arguments are given.
Function was a bit of a mess, use more sensible variable names and add comments.
Pedantic formatting.
No need to saying we are continuing if user tells us to.
If required=a is set in the option file, there is no need to print the N range to screen.

The user has not set this value in the file so to see it may confuse
as to what has actually been read from the file and what has been
calculated internally.
Check if an options is used more than once in the input file.

Warn if an option is repeated, but don't stop and use the
latest one.
Merge branch 'NewReadingOfInputs'

*Fixed an issue that occured if the -o argument was given and the -i wasn't.
*Refactored the reading of the option file to:
1. Read the values.
2. Confirm the values make sense individually.
3. Check that all options make sense when taken together.
Fall back to asking the user if any of the above fail.
*Future proofed the discovery of new nuclei by defining a MAX_Z and MAX_N
and using those in tests rather than 118 and 176.
*Tidied up setExtreme().
*Moved ConstructOutputFilename() so it is only ever called once.
Fairly big change to reading of command line arguemnts so bump version to 0.9.7.