If you sign the jar files yourself (third-party, as well as your own), you can simply add the necessary parameters to the third-party banks of manifest.mf (open them using the archive utility, that is, the archive manager on ubuntu or try 7-zip, etc. For Windows) add parameters as in your own jars manifest (repack them, on ubuntu it will happen automatically when you close the file after editing, I'm not sure that you are on windows) and then create an application / sign all banks.
This worked for me, although I'm sure there is a better way to do this.
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