Many updates; last version with smspatial.cpp main

removed agents_base class: fixes #9 (#36)

Co-authored-by: franticspider <simon.hickinbotham@york.ac.uk>

Working version with new checks and tests

This version has the following:

• script RunAllTests.sh runs the checks below on the code
• cppcheck: checks config and code - all warnings have been fixed
• smoke tests for "1 on 1", "Alife XII" and "smapatial" type experiments run - halt on fail
• catch.hpp tests now run automatically
• doxygen script generates documentation - in particular call-graphs

Thus the code base is set up for refactoring, allowing us to develop stringmol for future experiments!