groovy scripts executed from a URL are not run in a security sandbox

The fix for JAL-899 allowed groovy scripts to be executed by Jalview when their URL is passed in via the 'groovy' parameter. However, groovy scripts executed in this way have full access to the users machine, which is a security risk. A mechanism is needed to inform the user of potential risks, and if necessary, run the script in a sandbox (which can be done by passing in a java permissions object like : http://chrismoos.com/2010/03/24/groovy-scripts-and-jvm-security/ ).