Some more cleanup of things

This does a bunch of structural cleanups to make the code better

Renamed the test files so that their name gives a hint as to what it is
that they are testing, without having to open the file

Added a new test file, which tests how the body-inline multi-flags work

Pass to do some cleanup

Cleanup up some warnings that appeared

Pattern guards allow you to say that a particular pair should only be
replaced when the input matches a particular regular expression.

It is tied to the 'G' or 'Guard' control on the pair header, and is one
of the 3 or so major features I want to implement before a 1.0 release

As an aside, the other two features I want to add are:

Multibody Support
=================
This will allow a pair to replace to a few different things, based on
various conditions (the two main ones I want are some sort of cyclic
behavior, and some sort of guards for these)

Sub-application
================
Allow the application of a stage to the result of applying a pair/parts
of applying a pair. This will likely entail several sub-features such
as:

Named Stages
------------
A named stage is a collection of pairs that isn't applied by default,
but is instead used for convenient grouping of related pages together.

Custom Replacement
------------------
Instead of using replaceAll, I'll probably go for something using
appendReplacement etc. on Matcher and roll some sort of custom thing, so
as to provide for a convenient syntax for anything special I want to do
while running the replacement.

I'll also want to add some documentation, in addition to maybe doing
some restructuring to make how things are laid out more obvious.

All of the places that parse controls now use ControlledString instead
of doing their own stuff. -\(o-o)/-