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The MuPDF part is separated from the rest of the code as a completely separate file communicated to over web workers, so the separation means the rest of the code does not need to be open source.

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So that is not correct workaround at all for AGPL licenses. By moving the MuPDF logic into a Web Worker, you are still providing a "modified version" of the program to the user to interact with. The "separation" via a Web Worker does not change the fact that the user is interacting with a system that includes AGPL-licensed code.

Exactly.

It is a clear AGPL license violation without contacting the MuPDF sales team.

If the OP doesn't want to contact the sales team, it should be open source.

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