OS X 10.11 (El Capitan) makes changes to the handling of the /usr directory; as a result, 'configure' can no longer find my standard installation of XQuartz, which provides freetype headers and libraries.

The OS X installer removed /usr/X11R6, which is apparently where 'configure' was previously looking. (This is part of the System Integrity Protection feature [1], which also blocks future third-party installs from writing to that location.)

The files can be found in /opt/X11 -- this is the longstanding install location for XQuartz, with other paths consisting of symbolic links.

My system also has 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

[1] https://en.wikipedia.org/wiki/System_Integrity_Protection