Creating branch for API-related changes
Incremental save. CLI and ninjaArmy compile, working on ninja now.
Completed changes involving encapsulating WindNinjaInputs in ninja.
Forgot to commit with yesterdays stuff.
Probably half way done with changes to ninjaArmy. CLI updated to use new ninjaArmy interface.
Successfully building the GUI now with the new ninjaArmy interface.
Fixed some errors with misplaced function calls.
Updating the interface and added some constants to fetch_factory
Removed the option parameter for functions, deleted the old prototypes and refactored, working on implementation now
Finished implementing C API, everything is compiling, starting to test
adding doxygen comments
Added  centralized error definitions (ninja_errors.h), finished doxygen comments within ninjaArmy.h, fixed some linker errors I was having with C-to-C++, testing underway.
More testing of C API and minor changes along with that.
finished API testing, minor changes to ninjaArmy and the new API.
finished
modified error codes.
Merged latest trunk changes into the branch
fixed compiler/run errors
Finished merging changes from Levi branch, which includes the C API and refactored ninjaArmy class
move emissions stuff into dust/