I hit another snag in my project. I am building a runtime as a component of a cross compiler. Configure has to determine the various tools to use (denoted by passing --host=xx to configure), and I use all of the AC_PROG_XX macros. This may be an autoconf issue instead of automake, but what happens is that configure tries to test for the default extention of exe files. The compiler doesn't make exe files, however, because there is no runtime (chicken, egg).
Will automake be ok if I just do AC_CHECK_TOOL for gcc and g++ instead of AC_PROG_CC and AC_PROG_CXX?