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In eClipse select window --> preferences , click on JavaCard and then at the right side of the windows brows for your javacard kit SDKs in javacard home part,
now when you create a new javacard project, you can choose this version of javacard kit to use
You should be aware that you need to have a JCDK that matches the target card you are building your applets for. If you use a newer JCDK you may not be able to load you applets onto a smart card.