You could exec() to gcc with the -E option, to have it do
preprocessing only. I tried the following and it worked for both
includes and for macro expansion.

  Process expanding=Runtime.getRuntime().exec(
   new String[]{"gcc", // program name
   "-E", // Preprocessing (includes and macro expansion) only
   "-P", // Do not generate '#line' commands.
   "-undef", // Do not predefine any nonstandard macros.
   "-o", "expandedoutputfile.xml", // Where to put result
   "-nostdinc", // Search only directories specified with -I
   "-Idirectorycontainingfilestobeincluded",
   "-Ianotherdirectorycontainingfilestobeincluded",
   "-x", "c", // Treat source file as .c regardless of its name
   "inputfile.xml"} // The source file to be expanded
   );

This would also get you conditional compilation.

--Mike Amling