It's possible you just have a HDD that is getting up there in age and very gradually slowing down in preparation of failure. OTOH, it's possible the "genius" was full of it. Wouldn't be the first time someone at a computer store was talking out of their ****.
If you're prepared to do it, I say do it. You have almost nothing to lose, and if things don't improve, you can figure that it's probably your HDD slowly wearing out and decide whether you want to invest in a new drive or use this as an excuse to get a new computer. At least you'd have a good amount of advance warning so you can get everything backed up, and wait around for a good deal on a new drive. Replacing them on those units is pretty simple. Just take the battery out, there are three screws you loosen and then a metal flap in the shape of an L comes loose... From there you just pull the flap to slide the drive out, put the new drive on the little sled, put everything back, reinstall the OS, and you're good.
After years of service (since about 2006) my MacBook is slowing down.
When I run permissions repair, it takes about 30 minutes; then, when I open that utility again, it still says it will take about 30 minutes to run. In short, it appears that my many permissions errors are not being resolved by the utility.
My thought was to do a clean install and start fresh with a "like new" computer, but advice from an Apple Genius Bar person is that most of the stuff slowing down my computer and causing permissions issues will still be there.
Is this correct? Will a clean system install not take my hard drive back to the pristine condition I enjoyed on my first day of use?
My computer is a MacBook 1.1 with a 2 Ghz Intel Core duo processor w/2 GB memory; running OS X v10.6.8

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