Maybe I'm too dumb, but I haven't figured out a good way to sign just a binary (or a tar/zip containing a few binaries). I zipped up the binaries, sent them off to Apple, Apple comes back and says "yup, notarized!", and they still trigger the popup. I'm probably missing a step. I guess I'm not currently stapling the ticket to the binary, but supposedly you don't have to if you are running with a network connection.
You have to distribute a "bundle" in a particular directory layout.
you need to pay the tax, they are doing the 'pay money to reduce spam' solution
Theres two different steps, there is signing and there is notarization. You sign with the developer certificate using productsign/codesign, and then there is notarization, which you use notarytool to submit your signed binaray to apple to notarize.
finally you then take their response and staple it to your binary. Its a lot of steps.