Add support for multiple positional path arguments

This replaces #68. Instead of modifying `Prospector` to support multiple paths, I've modified `prospector.run.main` to create a new `Prospector` instance for each input path. 

Detailed changes:
* If more than one path is provided and one of the paths is a directory, raise a `ValueError`
* Explain multi-input directory restriction in `--help`
* Add `Path` to each summary
* Don't print `Messages` header if there are no messages