Redirect stdout and stderr to file when launched from getdown

When launched by getdown, jalview's stdout and stderr is not visible in the shell, or saved to file.

Getdown effectively cuts off the stdout and stderr.

Jalview should recognise when it is launched by getdown (the property "getdownappdir" should be set) and either create a default stdout.log and stderr.log and redirect system.out and system.err to those, or allow users to set these using -out and -err options.