Repairing permissions relevant to Apple apps. only?

Question

I installed Macromedia Flash Player 9 and Firefox 2 today, and tried to repair permissions because Firefox was running slow. I accidently selected the main disk rather than the partition, Macintosh HD, tried to repair permissions and got an error message saying that quitting would render the disk unusable, or something along those lines. I clicked stop repair twice and eventually had to quit out because there was no other choice. I hope this won't pose a problem later on, assuming that was the wrong disk to repair and it didn't go all the way. I'm slightly paranoid that my computer won't startup normally if I shut it off. Although I did restart after this happened and everything seems fine at this moment.
- Is repairing permissions really only necessary for system updates and Apple-based application updates (iPhoto, iTunes)?
- Also, should I try again or is it best to just let it go for now, since it was only third-party apps that I'd updated?
iMac G5 Mac OS X (10.3.5)

Answer 1

You are correct. Repairing permissions will have no impact on any applications or software that doesn't have a receipt saved.
When you are repairing your hard drive or permissions you should not quit the activity until it finishes. I recommend doing the following:
Repairing the Hard Drive and Permissions
Boot from your OS X Installer disc. After the installer loads select your language and click on the Continue button. Then select Disk Utility from the Installer menu (Utilities menu for Tiger.) After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer. Now shutdown the computer for a couple of minutes and then restart normally.
If DU reports errors it cannot fix, then you will need Disk Warrior (4.0 for Tiger) and/or TechTool Pro (4.5.2 for Tiger) to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
This may be overkill but it can't hurt anything.
Under normal circumstances you should not have to repair permissions. The reason you see it recommended so much is that it's a precaution that costs little to do and in some rare cases may actually fix something.