Window close handlers not called on Quit

The Desktop File | Quit option exits without first closing windows.
This means any close handlers are not called.
Mostly these are just freeing memory which will happen anyway.
A couple affect external resources:
- ChimeraViewFrame - offer option to close Chimera if it is open
- WebserviceInfo - cancel any cancellable running jobs
Questions arising:
1) should we give the user the option to shut down Chimera sessions (currently they are left running)?
2) would that be irritating if they had many open and were forced to choose for each of them?
3) do we want the option to leave web service jobs running between Jalview sessions (future feature?)