If you need the debug output of the puppetmaster running with passenger you have to uncomment this setting in the config.ru:

#ARGV << "--debug"

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If you don't know where your config.ru is, check the Apache DocumentRoot. It's in /path/to/DocumentRoot/../config.ru. For example if your DocumentRoot is /etc/puppet/rack/public/ the config.ru is in /etc/puppet/rack/config.ru.