refactor: rework coordinates#1832
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…mics/aind-data-schema into 1831-flexible-cs
…mics/aind-data-schema into 1831-flexible-cs
…mics/aind-data-schema into 1831-flexible-cs
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This PR adds the full suite of coordinate system definitions:
It deprecates the to_matrix functions which are no longer applicable if you use local frames (we were assuming global before).
And finally it deprecates the coordinate system library classes with Depth axes since those are now represented by local transforms.
A new coordinate_system_builder in the docs helps users construct their coordinate systems properly (more work to do there, but better to get it out and then make changes)