When saving warmup during optimization, also save the first sample.  Makes debugging easier.
Merge branch 'develop' of https://github.com/stan-dev/stan into feature/write-init-during-opt
Merge branch 'develop' into feature/write-init-during-opt

Conflicts:
	src/stan/gm/command.hpp
Implement saving the first sample during optimization in the new command.
Save the initial state during optimizaiton.
Merge branch 'feature/write-init-during-opt' of https://github.com/stan-dev/stan into feature/write-init-during-opt
Update .travis.yml to build docs in parallel.
Update .travis.yml
Merge branch 'develop' into feature/write-init-during-opt

Conflicts:
	src/stan/gm/command.hpp
Fix compilation error.
Merge branch 'feature/write-init-during-opt' of https://github.com/stan-dev/stan into feature/write-init-during-opt

Conflicts:
	src/stan/gm/command.hpp
Merge pull request #182 from stan-dev/feature/write-init-during-opt

Save the initialization state in the CSV file when doing optimization and saving warmup
Adding --vanilla flag to Rscript call, removing python and perl dependencies.
Merge pull request #373 from stan-dev/feature/issue-369-makefile-shuffling

fixes #369.
removing generated doxygen and manual
Merge pull request #383 from stan-dev/feature/issue-381-remove-manual-from-repo

Fixes #381.
Merge pull request #242 from ido/patch-2

Update .travis.yml to build docs in parallel.
Changed name from persistent sampler to fixed parameter sampler
Merge branch 'develop' into feature/persistent_sampler