How to codesign Mac OSX executable without changing code behaviour

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I have a java-based executable (generated from java wrapper tool) which works on Mac OSX.

I am now trying package it for deployment in a MyApp.app form, including codesign this to allow it to be accepted by GateKeeper.

However when I codesign my executable within the "MyApp.app/Contents/MacOS" driectory it changes how that executable runs - I get a ClassNotFoundException looking for the Java wrapper tool's specialised ClassLoader.

I realise this is probably an issue with the java wrapper tool's executable generation (and have raised an issue there), but is there was a way to avoid codesign impacting the executables operation? I can use signtool on Windows with no problem.

I have had a look at "--detached" as a codesign option - to sign and generate a detached signature file. But the codesign verify I'm using to test GateKeeper conformance doesn't recognise this - I get "...is not signed at all".

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