Rosyna Keller (some years ago):
Repair Permissions won’t touch any files in any of the user’s home folders since Installer.app can’t target user folders specifically, only any folder or a specific path, and there are no packages in ~/Library/Receipts/. The only way it’d ever touch any files in a user’s folder is if you installed something that let you explicity select a folder to install in (there are very few of those, none are available from Apple publically) and you chose a folder inside your user’s folder. The receipt would still be installed in /Library/Receipts/ and it would only affect the user that installed it. It also won’t fix permissions for any files that were created during the normal (or abnormal) use of OS X. This means it won’t touch any cache files, database files, swap files, or settings files not created by the installer. If a file isn’t listed in a receipt, it doesn’t exist to the repair permissions process. It’s really as simple as that.
In my experience, file and folder permissions get messed up all the time, just not the ones that Repair Permissions can fix.
The cedilla in this blog post’s host name is also a good test for your URL-handling code. My RSS reader app wasn’t able to open it, nor was the Open URL system service.
Update (2013-08-21): Thomas Brand:
Starting Mac OS X v10.6 and later, Disk Utility doesn’t even look in the /Library/Receipts/ directory when you Repair Disk Permissions. All it does is reset the Base Systems disk permissions back to the default as specified by version of Disk Utility you are using.
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