This work has been merged into HEAD.
However, the released automake 1.5 is still a little buggy for squid development. End users don't need automake installed, and those hacking squid for fun can use any automake version 1.5 or newer. Anyone submitting patches that involve regenerating the Makefile.in's needs to be using a specific version of automake to prevent a huge src/Makefile.in. The easiest way to achieve this is to apply this patch to your vendors source package for automake 1.5 and rebuild it. I.e. for RPM this rebuild your SRPM, for debian use apt-get source automake1.5, apply the patch, cd up a level and call apt-get --compile source automake1.5.