Disable redundant Archaeopteryx menu items and add Jalview related ones

Because Aptx was originally designed to be a standalone application there are still various options that can be selected in its menus that don't make much sense anymore. These are menu options like opening a tree or running a MSA.

An assessment of which menu items should be kept, ones that should be moved to the alignment view and which ones should be removed altogether should be made first.

In the same vein there are also useful menu items missing in Archaeopteryx that Jalview's original tree viewer has, mainly the option to sort the alignment by tree.