If the application contains any GPL code, the application all code must be distributed in accordance with the terms of the GPL. Exceptions are only part of the platform itself (Java in this case).
This does not mean that the code must be covered by the GPL, but it must be covered by a license that allows distribution under the terms of the GPL (LGPL, MIT, BSD, Apache, etc.).
You should refer to all libraries along with a description of where to get the sources. Most likely, these are installation instructions. If you distribute them through commercial activities, you must distribute (upon request) full sources, including libraries.
I'm not a lawyer though.
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