Add folder structure

[arsLibera]

Problem

Right now, (almost) all the source is contained in one big folder, aptly named "Source".

Solution

Good structure typically involves many files. That helps separate subroutines of the source, which is typically much easier to understand than a few massive files (usually a hallmark of a legacy code base and limited attention to architecture).

As the source is refactored, the number of files tends to grow. It usually becomes necessary to divide the files into groups using a folder structure. Some initial groupings I see are "Options", "Model", "FEM", "VTK", although I still have to better understand the details better to know what the appropriate groupings are.

We should consider updating the cmake to handle multiple source subfolders and moving some of the source into them.

Additional context

Future additional enhancement: Better yet, we should have each subfolder have an "export" folder, so that only exported headers will be available globally. Then, we can have local headers that are only available to that subfolder. This would be the start of a modular achitecture for better encapsulation. However, we would probably want to make all headers available to the unit tests (but that's not necessarily going to be required)

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