Selecting 'Keep in Dock' on a running Jalview desktop's icon in OSX doesn't work correctly

Launch a Jalview Desktop app on OSX
- the icon appears on the dock with a running indicator as the launcher starts
- a new icon appears in the dock, also with a running indicator as the Jalview app itself launches
- the first icon disappears

The main problem is if 'Keep in Dock' is enabled for the remaining Jalview icon after it is launched, when Jalview is quit the icon changes to an anonymous executable icon, and clicking on the icon yields a terminal window showing that 'java' was launched without any arguments. That's not what someone would expect to happen.

The second problem is that if 'Keep in Dock' is enabled for the Jalview Desktop Launcher (tricky to do but you can manage to do it because the launcher is updating Jalview), then you'll then have two icons.. one for the running Jalview and one for the Jalview Launcher. Again that's counter-intuitive for Mac users.

At the bare minimum, 'keep in dock' should allow someone to pin Jalview's icon to the dock for convenience. Right now it doesn't.