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Hi Rui,
If all your IDF files are in the same folder, just select all of them in the file selector dialogue using the Shift key or ctrl-A. You may also create a text file with a ".lst" extension and put in there all the idf file names, including the paths if they are in different folders, then select the list file instead of the idfs in jEPlus.
jEPlus v2.0's project file is in JSON format, which is quite easy to understand and manipulate. This gives you the third option to write the idf files to include in the project programmatically, and call jEPlus using its command-line interface...
Regards,
Yi