* Repurposed -OO so all sim run outputs including S_sie.resource are saved to the specified folder. The files are placed in the sub-dir either RUN_xxx or DP_Product of the specified folder.
* Updated for repurposed -OO.
* Added quoting code markdown for such as in order to show <name> as is.
* Added quoting code for missing items.
* Updated to raise an error when the --read-only-sim flag is used without the -O or -OO. Also made updates to the related document accordingly.
* Fixed the error message to be more clear.
* Replace sprintf with snprintf in all of Trick source. #1384
* Don't add -Werror for MacOS because of deprecated sprintf warnings which we cant get rid of because SWIG. #1384
* Fixed an unbalanced parenthesis in S_overrides.mk. #1384
Reorganized. Created a new top level include directory that will hold all of Trick's header files. Moved all of the Trick headers to this directory. Created a libexec directory that holds all of the executables that users don't need to execute directly. Changed all of the executables remaining in bin to start with "trick-". In the sim_services directories changed all source files to find the Trick headers in their new location. Since all of the include files are gone in sim_services, removed the src directories as well, moving all of the source files up a level. Moved the makefiles, docs, man, and other architecture independent files into a top level share directory. Renamed lib_${TRICK_HOST_CPU} to lib64 or lib depending on the platform we're currently on.
refs #63
