Fixed the version of tools.cli used by heuristomancer.
Modified the config stuff in clojure commons to support reading from a
file.
Modified donkey to add command-line options.

Added a setting for --help, --config, and --port.
Cleaned up iplant-email a little bit.
Modified iplant-email to use command-line settings.
Moved to newer tools.cli and added the --config option.
Merge branch 'dev' into cli
Added the ability to slurp the MANIFEST.MF file.
Added a --version option to donkey.
Fixed the version of tools.cli used by heuristomancer.
Modified the config stuff in clojure commons to support reading from a
file.
Modified donkey to add command-line options.

Added a setting for --help, --config, and --port.
Cleaned up iplant-email a little bit.
Modified iplant-email to use command-line settings.
Moved to newer tools.cli and added the --config option.
Added the ability to slurp the MANIFEST.MF file.
Added a --version option to donkey.
Merge branch 'cli' of github.com:iPlantCollaborativeOpenSource/DiscoveryEnvironmentBackend into cli

Conflicts:
	services/Donkey/project.clj
Added the git ref to the manifest.mf for the services.
Added the git-ref to the manifest.mf file for the tools.