Use first matched id in mo script
Remove superflous '#' script.
Remove command-line helpers, since they duplicate other tools and have fallen out-of-date.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.
Do not set MONGO_ORCHESTRATION_HOME automatically.
Use CWD as path for pidfile and log.
Use parent's parent directory to find "configurations" directory, if MONGO_ORCHESTRATION_HOME is unset.
Add "setParameter": {"enableTestCommands": 1} to all configurations.
README improvements:

Improve wording in REAMDE.

Remove documentation for command-line helpers from README.

Fix up examples section in README.
Add `curl` example and how to prettify JSON to README.
Add pip installation instructions.
Remove build status notification, since the Jenkins build doesn't currently work correctly.
Update README.md per move of 'configurations' directory.
Remove extraneous calls to logging.basicConfig.
Add links for requests to base URL and /servers.
Add /replica_sets links.
Add /sharded_clusters links.
Add apps/links.py
Restrict the scope of some of the links. Add at least basic links in sub-documents.