I tried to use the API and the sample program.... I added all the required jar files etc ...
however, when I added the SCUBA project I found that the program doesn't recognize the following packages in the SCUBA project :
do I have to include external tools such as JCOP tools ?
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.
I believe you need the offcard.jar file from JCOP tools. You can use JCTerminal to connect to either a real card or the emulator. As mentioned you do not need it to talk to a real card if you are using javax.smartcardio.* though.