Should you perform a clean install of Mavericks?
OK, so you can, but should you? Prior to Snow Leopard (OS X 10.6), I generally recommended a clean install. But the Snow Leopard installer and Setup/Migration Assistant were pretty good about not transferring over incompatible software, and subsequent OS X installers have gotten even better--in fact, Lion, Mountain Lion, and Mavericks even automatically detect some incompatible programs and system add-ons the first time you log in, as explained in my main installation article.
What about stuff the installer and Setup/Migration Assistant don't catch? In my experience installing 10.9 many times over a variety of existing Mountain Lion, Lion, Snow Leopard, and even Leopard installations, I've had little trouble that I could trace directly to incompatibilities with transferred code, and upgrading to Mavericks has gone even more smoothly than the many Mountain Lion upgrades I performed last year. (Last year, I said the same thing about upgrading to Mountain Lion compared to Lion the year before, but it's true! The process seems to get better each year.) Based on that experience, and similar reports from my Macworld colleagues, I feel comfortable saying that as long as you've properly prepared your Mac before installing Mavericks, you should be just fine installing directly over Mountain Lion, Lion, or Snow Leopard. (Because Mavericks, Mountain Lion, and Lion have so much code in common, upgrading from Lion or Mountain Lion to Mavericks seems to entail even less risk than upgrading from Snow Leopard.)
There are, however, a couple situations in which you might consider a clean install. The first is if you've done some funky partitioning of your Mac's startup drive that prevents the Mavericks installer from creating the special Recovery HD partition. Given how useful recovery mode can be, in this situation I recommend performing a clean install (with a good backup!) just so you can erase your Mac's drive and restore it to a standard configuration, thus allowing the installer to create the Recovery HD partition. (If you don't want to manually re-install everything afterwards, you can use Setup or Migration Assistant to transfer your data, applications, and the like from your backup to the new installation, as described above.)
The other is if you've been using your Mac for a while, installing and deleting many, many apps and OS add-ons, and your hard drive has become littered with lots of unnecessary gunk and cruft: orphaned application-support and preference files, abandoned preference panes, and the like. A new major version of OS X is a great opportunity to do some spring cleaning, so to speak. Of course, if you perform a clean install for this purpose, you don't want to use Setup or Migration Assistant to bring over everything from your backup--which will bring over all that cruft to your new installation. Instead, you should manually copy your personal data and then reinstall just those apps and add-ons you actually use. (Macworld contributor Joe Kissell talks extensively about such procedures in Take Control of Upgrading to Mavericks.)
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