I've found the root cause and the solution to this problem. I was using
puppetlabs' puppet modules to setup puppet agent and puppet master. The
whole setup puppetized the entire rack folder which contains config.ru.
The config.ru from the puppet module is the root cause as it does not match
with the new config.ru which is used by puppet 3
### Puppet 2.7.x config.ru
# a config.ru, for use with every rack-compatible webserver.
# SSL needs to be handled outside this, though.
# if puppet is not in your RUBYLIB:
# $:.unshift('/opt/puppet/lib')
$0 = "master"
# if you want debugging:
# ARGV << "--debug"
ARGV << "--rack"
require 'puppet/application/master'
# we're usually running inside a Rack::Builder.new {} block,
# therefore we need to call run *here*.
run Puppet::Application[:master].run
### Puppet 3 config.ru
# a config.ru, for use with every rack-compatible webserver.
# SSL needs to be handled outside this, though.
# if puppet is not in your RUBYLIB:
# $LOAD_PATH.unshift('/opt/puppet/lib')
$0 = "master"
# if you want debugging:
# ARGV << "--debug"
ARGV << "--rack"
# Rack applications typically don't start as root. Set --confdir and --vardir
# to prevent reading configuration from ~puppet/.puppet/puppet.conf and writing
# to ~puppet/.puppet
ARGV << "--confdir" << "/etc/puppet"
ARGV << "--vardir" << "/var/lib/puppet"
# NOTE: it's unfortunate that we have to use the "CommandLine" class
# here to launch the app, but it contains some initialization logic
# (such as triggering the parsing of the config file) that is very
# important. We should do something less nasty here when we've
# gotten our API and settings initialization logic cleaned up.
#
# Also note that the "$0 = master" line up near the top here is
# the magic that allows the CommandLine class to know that it's
# supposed to be running master.
#
# --cprice 2012-05-22
require 'puppet/util/command_line'
# we're usually running inside a Rack::Builder.new {} block,
# therefore we need to call run *here*.
run Puppet::Util::CommandLine.new.execute
Changing the config.ru resolved all my problems above
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