Bug fixes: jsonconfigparser.utils.dict_ and jsonconfigparser.shell.run

Fixed error where jsonconfigparser.utils.dict_ would explode and attempt to rebuild secondary dictionaries, added test confirming fix. Fixed shell from blowing up when certain errors are thrown, more robust error handling is required still

Added MANIFEST.in and corrected setup.py (still complains about unknown options: test_requires and exclude_package_data, which I was under the impression *were* valid options).