Some suggestions (sorry for my english) :

Tree panel :
- Auto collapse all unecessary chapter
- Green arrow always visible
- Highlight the path to the current page (ex: part 1, sub part 2, sub sub part 2 = 3 lines highlighted)

Navigation :
- Take a screenshot of the content and reduce it in a closeable window in the top left/right corner, increase it on mouse over, reduce it again on mouse out, useful if a long text talk about a previous illustration.

Thanks.