sequence associated alignment annotation not added to an alignment is not saved to project

This problem arose in the context of sequence associated rna secondary structure, which is (currently) not displayed on the alignment, but instead available for visualization in VARNA via the 'view structure' sequence ID popup submenu.

Unfortunately, the jalview project marshalling code uses the Alignment's alignment annotation list to decide what to store for each view. That is - if a sequence's annotation is not added to an alignment (where it may be marked as hidden), then the annotation will not be stored.