adding src/stan/math/functions.hpp
rearranged stan/agrad/rev/ to match stan/math/
Merge branch 'feature/issue-440-log-prob-for-eigen' into feature/transition_samplers_to_eigen
Move from std::vector to Eigen::VectorXd e'rywhere
Whoops, forgot the all important new agrad file
Merge branch 'develop' into feature/transition_samplers_to_eigen

Conflicts:
	src/stan/gm/command.hpp
rearranged stan/agrad/fwd/ to match stan/math/
Merge branch 'develop' into feature/transition_samplers_to_eigen
Fix mcmc_writer header and tests
Fix the MCMC tests
Fix sample test
Fixed grad includes
Fixed Welford tests
Fixed hamiltonian and integrator tests
Who likes int/unsigned int conflicts?
cleaned up top-level stan/agrad/*.hpp includes
Merge branch 'develop' into feature/issue-443-reorganize-agrad

cessary,
Added base hamiltonian test
refactored init_adapt function to call a simpler init_adapt function that can be called through tests
adding a test that fails for init_adapt<>