Update definition of tree depth: #296

Summary
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Update definition of tree depth to count partially completed subtree
and not just fully completed subtrees.  Also included an explicit
count of number of leapfrog steps computed.

Intended Effect
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Slightly different behavior in treedepth__ diagnostic, new
diagnostic n_leapfrog__.

How to Verify
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Run any model, note that 2^{depth - 1} - 1 < n_leapfrog < 2^{depth} - 1.

Side Effects
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stan_csv_reader_test is deprecated, but this was an existing issue.  Otherwise unit tests pass.

Documentation
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Introduction and Command chapters updated.

Suggested Reviewers
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Anyone.