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CMakeLists.txt should be standardized #32

@jcfreeman2

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@jcfreeman2

Things like:
-Removal of the nonstandard set(INCLUDE_DIR "include/snbmodules/")
-Removal of variables which don't get used (e.g., tests)
-Adding build of code currently ignored (like the executables in test/apps, unless we want to get rid of that code entirely)

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