BIG REFACTOR. Moved all remote/API logic to lib/api, for consistency.
Moved lib/agent/keys logic to lib/setup. Uses the api module too.
Updated conf module with new API changes.
Require rimraf in package.json.
Fixed load paths.
Moved package/updater logic to ./lib.
Whitespace.
Function position.
Removed entry requires.
A few additional checks.
cli_spec and conf_spec.