Gets rid of some indirect inclusions in cpp files.
Also this will reduce the amount of rebuilt files if
changes occur in the DataReader header.

Also remedies places where the video backends and core rely on things
being indirectly included.

Approximately three or four times now, the issue of pointers being
in an inconsistent state been an issue in the video backend renderers
with regards to tripping up other developers.

Global (ugh) resources are put into a unique_ptr and will always have a
well-defined state of being - null or not null

They were only called at once, so no need to seperate them.

This also removes the only dereference of the NativeVertexFormat in VideoCommon, so backends may just return nullptr.

It may be a bit weird to see calls to static functions in
VertexManagerBase now, but at least it's easier to see what's going on.

Various fixes to formatting and whitespace

Instead we keep the loaded vertices in CPU memory.

Also:
 * Implement support for per-vertex PosMatrixIndex
 * Only update zslope constant once when zfreeze is activated.
 * Added a bunch of comments.