The OS X El Capitan installer cleans out the /usr directory, including /usr/X11R6. This is part of the System Integrity Protection feature [1], which also blocks future third-party installs from writing to that location.
Result: configure breaks when it can't find freetype, even after I've re-installed XQuartz. The files can be found in /opt/X11; there's also a symbolic link from /usr/X11 (I'm not sure how that came to be, or why the config script doesn't try it). Workaround: sh configure --with-freetype-include=/opt/X11/include/freetype2 --with-freetype-lib=/opt/X11/lib —Dan [1] https://en.wikipedia.org/wiki/System_Integrity_Protection
