Save Aptx as part of Jalview's project file

Current Jalview trees are saved in the Jalview project file, the Aptx tree will need this same functionality.

Attention will need to be paid to allow project files that contain the old Jalview tree viewer to still be loaded in, as these trees are essentially stored in the Newick format Archaeopteryx could directly load them in and re-associate the nodes. Ample testing will also need to be performed to check how Aptx handles being reinitialised, does it corrupt data or its GUI, are (possibly internal) nodes still mapped correctly etc.