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security/yubikey-manager-qt/files/patch-resources_linux_AppRun
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You should not hard-patch /usr/local
and then to a ${REINPLACE_CMD} 's|%%PREFIX%%|${PREFIX}|' ...
.. so in the end, you could just drop this patch, and just do the ${REINPLACE_CMD} of /usr/bin/ykman-gui to ${PREFIX}/bin/ykman-gui.