Refactor manager_factory.py for consistency.

Breaking configuration and building stages out adds some consistency for how the default manager is constructed and will allow configuring managers via other mechanisms then the job_managers.ini file more easily (namely app.yml).
Allow configuring job managers in app.yml.

Can specify a dictionary of managers of the form:

managers:
  name:
    type: queued_drmaa  # defaults to queued_python
    option1: value1
    option2: value2

or just a single default manager with

manager:
  type: queued_drmaa
  option1: value1
  option2: value2
Fix typo Nate caught in Galaxy.
Update Galaxy utilities classes through Galaxy changeset 5fac4d4.

Various fixes, doc updates, etc... as well as allowing dependency_resolvers_config_file and job_metrics_config_file to point at YAML files.

https://bitbucket.org/galaxy/galaxy-central/commits/5fac4d4b7d7d6b056056bf2a6094c7777dc28a71.
Merge pull request #14 from jmchilton/config

Allow configuring job managers in app.yml.