I assume the mere act of copying the license (a file called devel.lic which is a small text file) is causing this.
Yes. Any change to the application bundle after signing could trigger this. I think there are ways to validate a signature while accepting a certain level of irregularity. But you don't have any control over how the OS on an end user's system is going to perform the validation. And those validation strategies will likely change as the OS evolves. The best course of action is to always assume the bundle never changes.
There are many alternative places to store licensing information. I recommend keeping it in the user's home directory so you don't have to ask the user for admin privileges to create it.
Why does it say it “does not seem to be an app”?
Most likely the bundle structure diverges too far from what is expected.
Remember that the purpose of all of this is to detect and block malware, which often uses novel ways to structure bundles and executables. The idea is to exploit edge cases that Apple never anticipated in order to confuse the system and gain more privileges. The more unusual your app is structured, the more likely you are to be impacted. This can happen during development or at an unexpected time later on.
This self-modification of the files in the Contents/Resources directory is a huge feature. We allow downloading of patches, which add features and fix bugs in the product. Is this going to be a problem, going forward?
Yes.
In theory, it's possible to modify parts of the application bundle and then supply an updated signature that matches the new bundle. But I'm not sure if anyone has ever managed to do that successfully. It's a high-risk, high-effort solution when storage and bandwidth are cheap.
Furthermore, you shouldn't be putting patches or executable code in the Resources directory. That is a special location for non-executable resource data. Using it for any kind of executable code is an excellent way to give yourself signing and/or notarization problems.
Topic:
Code Signing
SubTopic:
General
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