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.
fixes #372. Removing compiler warnings. Mostly unsigned int and unused variable warnings.
doxygen: squashing as many warnings as possible.
Merge pull request #409 from stan-dev/feature/code-clean-up

Feature/code clean up