Update option parsing to popl.hpp

[graeme-a-stewart]

Using getopt_long for options is quite clunky and awkward, e.g., the syntax for options is poor, no support for proper default values and no generation of a --help text.

We could replace it with popl.hpp, the Program Options Parser Library. It addresses all of the defects above and it's a single header file that we can have in the repository, so there is no additional dependency (c.f. Boost.Program_options).