update to documentation
changed to more standard make variable names
changes to make system -- still need to update examples
changed over the examples
clean up of make system
fixes to make sys
more make sys update
additional make sys fixes
changes to make system to support multiple options ect..
removed KIM_API_DIR from make system
moved makefiles into subdirs added linker defaults
added templates to append to compiler flag settings in Model make files
updated documentation for makesystem changes