Martin Lippert added a comment in Pivotal Tracker:
I tried to find another solution to this in the Equinox launcher code, but failed. Gatekeeper seems to do this path randomization action after every restart of the machine. Therefore the launcher just don't know whether it is indeed a newly installed app or "just" a newly randomized app.
I detailed all my results in:
So please, to avoid this, move the STS.app bundle to a different location using the Mac Finder. It looks like it doesn't have to be the "Applications" folder, it can also be a different one on your drive (whatever fits your needs).
If you want to verify that the app isn't moved by Gatekeeper, you can dive into the configuration details by going to the About dialog, select the Installation Details, click on the Configuration tab, and look for the "eclipse.home.location" property. It should point to the path where you put STS. If it starts with "/private/var", then Gatekeeper has moved the app to a randomized read-only location.
I hope this helps.
Side note: we might change the packaging of STS in the future and put it into a signed DMG file, so that our users have to move it to a location on their disc.
View this Pivotal Tracker story: https://www.pivotaltracker.com/story/show/132322379