macOS Sierra Missing App Icon in Dock and "Check for Updates..." Fails for Certain Apps
Solution 1:
Specifically regarding the warning you are seeing, from Rogue Amoeba:
Gatekeeper Path Randomization ... works by mounting a read-only disk image in a temporary path in the file system, copying the app onto that disk image, then launching the app from there.
GPR is a new security feature in Sierra intended to close a loophole where malicious programs could be packaged with Developed ID-signed legitimate programs, and thereby bypass Gatekeeper security intended to prevent unsigned applications from running.
GPR is disabled after an application is moved to the /Applications folder, however software update systems will fail, because when the new version of the app is downloaded, it has to be moved by the user before it will execute outside of the read-only disk image imposed by GPR. Therefore the best way to update is to download an updated copy of the app from the developer's website and manually move it to the /Applications folder.
Solution 2:
Cause: Gatekeeper Path Randomization introduced by macOS Sierra.
Steps to Fix:
- Run command:
xattr -dr com.apple.quarantine /Applications/Your.app - Drag app back to Dock;
- Restart Mac.
Consequence:
- App icon stays at Dock after restart
- Check for updates works