Its was impossible (at least for me) to keep the windows in sync without bloating the code too much.

See b957d0b8

Might be better to use one variable with different values.

And emit 'fragmentchanged' with the appropriate fragmentData to show or hide fragments.

It's pretty nice to have markdown in slides. It's even nicer to have
markdown in speaker notes too :)

It can be tedious to load up the speaker notes, with the whole having to
open the javascript console, and clicking on the link.

This simplifies it by automatically opening the notes in a new window.
Most browsers will warn that it's trying to open a pop-up, but it's easy
enough to allow it.