Stockholm format parser/writer

This is in the new parse format that @ElDeveloper created in #235 so merge his first.
These references are not formatted correctly. Should be:

```
.. [1] http://sonnhammer.sbc.su.se/Stockholm.html
.. [2] http://en.wikipedia.org/wiki/Stockholm_format
```

Then, edit the *Notes* section to look like the following:

```
Notes
-----
If references are included in GF data, the RN lines are automatically
generated if not provided.

The Stockholm format is described in [1]_ and [2]_.
```