unify behaviour of groovy scripts when called via CLI, run from Groovy console and calculate 'run script' menu

Jalview running headlessly has a slightly different groovy scripting environment and certain UI calls don't work compared to when running scripts interactively.

Ideally we need a consistent api that works regardless.

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originally this issue reported some problems with scripts demonstrating custom programmatic file format or colourscheme registrations that were identified when groovy was updated (JAL-4304).