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I am distributing a free, closed source Java application which includes some unmodified third party jar files in the package (under a lib folder). These third party jar files follow one of BSD2, Apache2, MIT licenses. I have copied the respective licenses as well in the package. Now I have to include one license for my product as well.

My doubt is, should my license cover the entire software product, including the third party libraries. Or should I write it in such a way that my license applies to only my own set of files and mention that the third party content is covered under the respective license files included in the package? Basically, what should be the "Software Product" in my license?

If it is the first option, I believe that I will not be able to include explicit terms for my own binaries (eg: no commercial redistribution), which may violate the license of included libraries. If it is the second option, are there possibilities of ambiguity about the accountability of the software's actions as a single whole product?

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You can do either. Apache and MIT both explicitly give you the right to sublicense the work provided that you comply with their terms, so "including terms that deny commercial redistribution" will not violate those libraries' licenses. (Don't forget Apache 2.0 Section 4d about the NOTICE text file!) BSD isn't as clear, but I think that's implied. You could just package everything up as proprietary.

On the other hand, if the libraries are sufficiently separable from your software, you don't have to do that. There shouldn't be any questions about the software's actions as a whole because all three of the licenses you describe disclaim warranty and liability.

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