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
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?
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<>
fixed code to take in the appropraite starting value for init_adapt
removing compiler warnings
Merge pull request #446 from stan-dev/feature/transition_samplers_to_eigen

Feature/transition samplers to eigen
Merge branch 'develop' into feature/issue-449-fix-initialization
merging develop. changing std::vector to Eigen::VectorXd