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While the JavaApplicationStub binary itself is signed, the resources don't appear to be signed. I get the same error preventing me from loading the program at all from Finder (though running either the jar or JavaApplicationStub from the terminal is still functional). If I overwrite that...

There's minimal difference cryptographically... I don't believe it's trivial if at all possible to give full trust to a self-signed key, but once a given app is opened via right-clicking, that app will work unless it's modified again, avoiding the potential for say, for example, malware to...

Signing the binaries with a self-signed key is enough to allow the file to be right-click->open'd and from there on, simply opened normally... I made myself a self-signed certificate called "codesign", with extendedKeyUsage=codeSigning, ran codesign -s codesign -f KoLmafia-15.7.app, and was good...