Updated Nepho to bootstrap hooks and handlers

Updated Nepho cli code to use the bootrap method to initialize hooks
and handlers. This is related to issue #88. For reference look at
the comment in the issue and this link
http://cement.readthedocs.org/en/latest/api/core/foundation/#cement.core.foundation.CementApp.Meta.bootstrap
Added more tests, and working on getting a full list
Cleaned up some format errors
Cleaning out tests so that we have one working example

Cleaned out tests that were breaking the build, and left in a single
working example. I'll add more tests in after we pull in the
cli/bootstrap code.
Merge pull request #159 from tfhartmann/88-cli-bootstrap

88 cli bootstrap