I have the following setup in my phpstorm, and I would like to combine my javascript files located in the /js/app and /js/lib folder.
now it's only minifying a single jar, I would like to combine them

One simple way to do it:
--js file1.js
--js file2.js
--js_output_file all.min.js
** Since you want it to operate on js files from different directories you may have to modify the file paths and "Working Directory" option for it to work properly.
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