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
Tweaked NUTS algorithm with correct behavior at each subtree
updating argument configuration test to not generate 'good' and 'samples.csv' in the working directory
updating test/gm/command to not leave any files in the working directory
broke apart src/stan/command/print.cpp to the main and functions. added unit tests for next_index and matrix_index. made those two functions safer.
updating cmd_line to allow for spaces in string arguments
Merge branch 'develop' into feature/issue-185-command-line-handle-spaces
Merge branch 'develop' into feature/issue-280-bin-print-blowing-out-memory
Merge pull request #311 from stan-dev/feature/issue-310-test-unit-littering

Fixes #310.
Merge pull request #328 from stan-dev/feature/issue-185-command-line-handle-spaces

Fix to stan::io::cmd_line to allow spaces in string arguments
Added compute_criterion unit tests
Added built_tree unit tests
Merge pull request #327 from stan-dev/feature/issue-280-bin-print-blowing-out-memory

Fixed unsafe code in bin/print
Remove deprecated cout
fixes #337. Builds Stan in 64-bit mode.