My daughter, explaining why she was reluctant to upgrade her OS if not necessary, complained that a previous upgrade resulted in the computer reporting a program as damaged when the only thing wrong with it was that it was not from the Apple Store or an identified developer. A web search for the text of the message eventually provided her the explanation—to run the program she had to change her security settings to permit applications downloaded from anywhere to run. Prior to upgrading the system (to OSX 10.8.5) the program had run with no message, so she concluded that the upgrade had either added a new "feature" or altered the security setting without telling her it was doing so.
My initial reaction was skepticism. While I could understand Apple warning a user against a program not from a trusted source, describing such a program as damaged is a lie. The appropriate response would be a warning that the current security setting will not allow the program to run because it is not from a trusted source. That would allow a user to decide whether or not to change the security setting. The result of reporting the program as damaged could well be to cause the user to waste quite a lot of time trying to locate an undamaged copy.
I have now checked her report, and it was correct. My desktop is also running 10.8.5. I set my Security & Privacy settings to "Allow applications downloaded from Mac App Store and identified developers." I went to the site
for maptool, the program with which she had encountered the problem, and downloaded maptool-1.3.b89.dmg. When I double clicked on the maptool program on the disk image, I got a message:
"MapTool-1.3.b89" is damaged and can't be opened. You should eject the disk image."
I then reset my security settings to "Allow applications downloaded from: Anywhere" and double clicked on the program. I got a warning that it had been downloaded from the internet, clicked the "open" button, and it opened.
Apple is in fact deliberately lying to its users.