finished manual for next version other than possible addition of fake data and posterior predictive chapter
fixed refresh doc by removing refresh=0 and adding redirect to /dev/null option
Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-485-next-manual
fixed all outstanding bugs and added all requested clarifications
Stop using write_csv and write_csv_header during optimize.
Speed up reading R dump formatted files by:
- Prevent constant reallocations of std::strings
- Convert to using boost::lexical_cast instead of stringstream
Merge branch 'develop' into feature/issue-532-remove_write_csv
added new functions to stan/gm/command.hpp; write_iteration_csv, write_iteration; both unit tested
changing command.hpp to use the write_iteration function
changing command.hpp to use the write_iteration function
many updates to manual including identifiability chapter
slight revision to identifiability based on comments from Ben
resolved acknowledgement conflicts
updated problematic posteriors section, removing identification references
fixed correlation_matrix_test.cpp
Merge branch 'develop' into feature/issue-532-remove_write_csv
Merge pull request #550 from stan-dev/feature/issue-549-fix-correlation_matrix_test

Fixes #549.
finished problematic posterios chapter, updated hoffman-gelman in press to 2014
adding optimization output test. fixed newton method so it actually runs
removing last remaining call to write_csv