EmacsWiki (at http://www.emacswiki.org/emacs/FlyMake ) has a recommendation to create a flymake.mk file and include it in every Makefile if you use Automake, but that doesn't seem very ... Automake-y and I guess that having a standard m4 macro for this would be a better solution. I was wondering if anyone had seen such a wild beast in the wild before I left and took into my mind what I had built myself.
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