The AC_CHECK_HEADERS does by default use the CPPFLAGS and not the INCLUDES variable to check for headers. So, if you define all header paths in INCLUDES, they will not be found by AC_CHECK_HEADERS, and thus headers like udunits2.h, gshhs.h located in private locations will not be found even if --with-xyz=/location is given.
I have successfully replaced all INCLUDES with CPPFLAGS (including the PYTHON_INCLUDES to PYTHON CPPFLAGS) in the configure.in and could configure and compile gdl. I also recommend to replace the udunits2/udunits2.h with simply udunits2.h or allow both header locations since both are common.
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