Remove legacy global variables

[timothy-nunn]

There are several bits of legacy functionality (controlled by global_variables which should be removed)

run_test

1. Any useful 'tests' should be moved into the test suite and removed from the main code. (Test can be found by looking for if global_variables.run_tests == 1: or similar)
2. run_tests should be removed from the global variables data structure, inputs, etc.
3. Any references in the docs should be removed

verbose

Anything that was 'verbose' before should either be removed if not useful or logged.