This re-works the way that CLI options are passed through to the
analyzer so that they can act as overrides for config options. If
not given on the CLI, options will come from a config file. If no
file is used then a default value is chosen.
Two lists are also populated with tests to include or exclude.
These lists are not used for now but will eventually replace the
way we select test to run in a future patch to follow.
A CLI option can now be given to tell GAS it should parse data
from a JSON file. Fatal errors are given if the file is not
readable or is not valid JSON.
The logic around annotations (nosec) was broken, meaning they were
ignored by default and would not skip sub-blocks. This fixes the
problem and also adds a test to make sure it wont be broken in the
future. Closes#25
