>> 1. I can't get automake to read a dynamically created AC_OUTPUT
>> parameter list. This is correct behavior but how do I specify
>> which files it should create?
Yes, automake needs a static AC_OUTPUT list. Automake uses the
argument to AC_OUTPUT to determine which Makefile.am's to scan.
My suggestion: keep AC_OUTPUT static, and use dynamic SUBDIRS to
decide which directories not to build.
>> 2. The extension semantics does not enable me to use features of GNU
>> Make like conditional statements, useful when not all compilers
>> support dependency output. Automake chokes on shell errors when
>> having "ifeq" statements in Makefile.am files.
Yes, automake does not allow this either. One goal of automake is to
produce portable Makefiles. GNU make conditionals are not portable.
Tom