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It turns out that IDI, GWM, GKS and CCDPACK were not explicitly adding the X11 includes path to the compiler options. This was noticed when OS X Mountain Lion stopped adding /usr/X11/include to the build automatically. We now add $X_CLAGS to AM_CFLAGS or equivalent. GKS was also tweaked to stop the build early if X11 was missing rather than stopping the build when the xwindows driver was being built. This was partly driven by the global GKS configure.ac not adding X_FLAGS to includes before attempting to check whether X11 includes were available.
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