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Suppose I want to add a runtime conditional to a Makefile generated by Automake. Is there any way to tell Automake about this conditional?

+1  A: 

You've asked a pretty general question so I can only provide a pretty general answer. Your project's Makefile.am is what automake parses to produce the Makefile.in file which ultimately produces the Makefile. You can generally just add your custom rules to Makefile.am for most cases (assuming this is under your control). See here for more details or google Makefile.am

bjg