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No, it should be possible to build the relevant projects without relying on the JCOP tools if you don't have a need to work with the JCOP emulator. Please PM me at firstname.lastname@example.org for instructions.
PS Not sure if OTN is the best forum for JMRTD specific questions. Consider asking them on the project's open discussion forum over at SourceForge: http://sourceforge.net/projects/jmrtd/forums/forum/580232.