Remove command-line helpers, since they duplicate other tools and have fallen out-of-date.
ignore the pid files
remove executable bit from things which do not need to be executable
Update setup.py and README.md per removing shell helpers.
Update project author.
Include "configurations" directory as part of mongo_orchestration package.
Fix paths to point to new location of "configurations" directory.
Merge pull request #124 from lovett89/install-configurations

Include "configurations" directory as part of mongo_orchestration package.
Add "setParameter": {"enableTestCommands": 1} to all configurations.