Updated API documentation and optional plug-ins (#92) implemented.

Hi guys,

This implements #92 and looks like this:

```python
import pyblish.main
pyblish.main.publish(include_optional=False)
```

`include_optional` defaults to `True`, meaning all plug-ins will be processed, unless explicitly told not to.

### API Documentation

The change can also be seen in the new API documentation, once the request has been merged.

- http://docs.pyblish.com

The API documentation is meant to provide guidance for developers implementing plug-ins or extensions using Pyblish. Each member documented here is accessible via `pyblish.api`

Best,
Marcus