I have exactly the same problem with Qt frameworks, they have Versions/5 instead of /Versions/A
In an earlier post it was asked how to coerce Xcode to use the right (Current) version?
Apple's Code Signing Guide says:
Important: When you manually code sign a framework, only the current version, the one pointed at by the Versions/Current symbolic link, is signed by default.
Why Xcode does not follow this?
Hospodar
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I have the same issue. I have a QT application with QT frameworks with single version of 5.