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See http://wiki.netbeans.org/JavaCardTODOs - in order to implement issue 170667 the Ant task that does packaging needs to generate the javacard.xml correctly. Currently it uses a source file provided by the project templates.
Anki, any progress on this?
First this issue is applicable to classic applets only. I don't see the point for generating and replacing META-INF/javacard.xml for classic applets. The best way is don't generate this file in new Classic Applet Project. See my comment to issue 170667.
javacard.xml no longer generated for Classic Applet and Classic Library projects.