Break up handleUserArgs() into multiple functions.

index.js
	-Refactor `handleUserArgs()`, by moving its flag-specific
	code into two new functions, `examine()` and `remap()`.
	-Cuts down on the verbosity of `handleUserArgs()`, and is a
	necessary change for an upcoming change to how the tool
	interprets rules files (namely, using `eval()` instead of
	`require()`).