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Hi, I'm trying to add my custom encryption for files on storage, but I've several doubts:
Yes you need to create a JAR containing your code. To build the JAR you will likely use Maven and therefore need proper dependencies on the base Nuxeo JARs containing the interfaces you implement and the classes you extend. This is standard Java/Maven development. Please start at https://doc.nuxeo.com/corg/ if you're not familiar with the process.
And yes you will then have to change the configuration to use your class instead of the standard one.
Note that Nuxeo already contains an AES-based encrypting binary manager, see https://doc.nuxeo.com/nxdoc/implementing-encryption/ for more.