Refactor toward support for running Galaxy in docker-galaxy-stable.

 - General cleanup of planemo.galaxy.config docstrings and such.
 - Refactor the configured Galaxy properties into ones relevant for Docker and not.
 - Create an interface for the GalaxyConfig object to be very explicit about what the rest of planemo expects from it.
 - Reduce this interface - mainly involves refactoring startup command generation so pid_file doesn't need to be used outside the config module.
 - Implement a BaseGalaxyConfig for GalaxyConfig object functionality that will be shared with a future Docker impementation - and put the local instance specific stuff in a LocalGalaxyConfig object.