Tweak NUTS acceptance statistic, introduce number of divergent iterations for diagnosing adaptive HMC implementations
Merge branch 'develop' into feature/improve_nuts_diagnostic

Conflicts:
	src/stan/mcmc/hmc/nuts/base_nuts.hpp
Update sampler param name to be consistent with doc
Update sampler param name to be consistent with doc
Update model tests to ignore new diagnostic
Merge pull request #388 from stan-dev/feature/issue-323-size-decl-types

Fixes #323.
Merge branch 'hotfix/v2.0.2' of https://github.com/stan-dev/stan into hotfix/v2.0.2
Fixes #275. Removing unused trunc_normal distribution.
Fixes #344. Removing src/stan/math/matrix.cpp
Fixes #407. Moving src/stan/agrad/fwd/phi.hpp to Phi.hpp
Fixes #408. Added a variable for 32-bit builds in Windows. Added doc.
Remove last reference to n_divergence
fixes #372. Removing compiler warnings. Mostly unsigned int and unused variable warnings.
added two tests that fail in gamma_q chain calculations
doxygen: squashing as many warnings as possible.
refactored code. The same implementation was in src/stan/prob/internal_math.hpp. This doesn't solve the infinite loop problem.
Merge pull request #409 from stan-dev/feature/code-clean-up

Feature/code clean up
Fix header guard for mock_hmc.hpp
analytic gradients for sd, variance, new vari impl for stored gradients, plus tests, doc
Merge branch 'develop' of https://github.com/stan-dev/stan into develop