Feature/transition samplers to eigen

Summary
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Leverages the changes from #444 to transition internal storage from std::vector to Eigen::Vector.  Touches the samplers, MCMC I/O, autodiff, and command.hpp.  Additionally the discrete parameters have been removed.

The optimizers and diagnostics have not yet been transitioned.

Intended Effect
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No user-facing changes.  Code should perform exactly as before.

How to Verify
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Run any model with the same seed before and after to validate exact same result.

Side Effects
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A bunch of tests that interface with the samplers directly will likely break.  I'm ready to fix them as soon as possible.

Documentation
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No changes.

Suggested Reviewers
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Anyone.