File→New: don't change the scratchpad bg

The scratchpad is an independent document.
File→New was updating its background to match the main doc default,
which is ugly and side-effecty.
Remove/replace deprecated API

Remove deprecated API calls and properties from lib.document.Document:

* layer_idx
* doc_observers
* layers
* layer
* get_current_layer()
* set_background()
* render_as_pixbuf()

Replacing any remaining usages of them.