Futher refactoring for TiddlyDesktop

We need finer control over the boot process so that we can force it to
load tiddlers from the Node.js file APIs rather than from the DOM
Switch to using `$tw.fakeDocument` for the fakedom document object

So that we can free us `$tw.document` to be the actual DOM document
Improve logic for initialising reading node tiddlers

We want fine control of whether tiddlers are read from the DOM or the
file system, without ganging it to whether we’re on node vs. browser.
Move node-webkit saver into a plugin

We don’t need it for TiddlyDesktop now that it reuses the TiddlyFox
saver. But it is still useful for embedding a TW directly into a
node-webkit app
Add link to French thesis notebook