fixes #2085 - load Puppet 3 app defaults for master mode too

Allows $confdir and other run mode specific settings to be initialised from
the defaults present in Puppet::Util::RunMode.  When requesting detail on
classes, the Puppet parser indirectly requests app level settings so both
global and app settings are needed.  Refactored into shared code for both
parser and environments to use.
Fixes #2143: Only create the log file parent dir if daemonize is true
refs #1567 - fixed a copy paste error
version bump to RC3
fixes #2101 - add bundler / Gemfile
Fix a number of tests and settings so tests run from example settings.yml

- enable subsystems being tested before proxy loads code
- fix test assuming /bin/ls is always first in PATH
- dummy puppet.conf file