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Currently, abstract-php.rb has /usr/local hardcoded in couple of places, as homebrew prefix. That's the default prefix, but it's not the only possibility.
$ ack -Q '/usr/local'
251: args << "--with-mysqli=/usr/local/bin/mysql_config"
252: args << "--with-mysql=/usr/local"
253: args << "--with-pdo-mysql=/usr/local"
388: Mountain Lion comes with php-fpm pre-installed, to ensure you are using the brew version you need to make sure /usr/local/sbin is before /usr/sbin in your PATH:
Use real homebrew prefix. Closes #371