Rework configuration system

[skmp]

• Missmatching argument vs env values
• Two layers of mappings that we don't really need to go through
• Factor common code out of FEXLoader, IRLoader, TestHarness, etc
• Add command line option to ignore any other layers (for CI, tests)
• Don't flatten default values / provide specific default values (possibly "default?") for easier config migrations
• Add configuration versioning for future automatic config migration