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Improve documentation and code style #2

@rafe-murray

Description

@rafe-murray

Summary

Only some of the files have comments documenting the methods within. There is also a significant amount of code that has implementations in header files.

Desired outcome

All method declarations have a comment above that documents the purpose, parameters, return value, and any pre- or post- conditions in some header file. All method definitions are moved to .cpp files (and all method declarations moved to header files).

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