[Editor's note: This article is part of our series of articles on installing and upgrading to Mavericks.]
It used to be that when upgrading to a major new version of OS X, installing over an existing OS X installation--for example, installing 10.3 over 10.2--entailed some degree of risk, as existing applications, add-ons, and support files could conflict with the new OS. For this reason, many people used to perform a "clean install": wiping your hard drive (after backing it up, of course), installing the latest version of OS X, and then either using Setup/Migration Assistant to restore your applications and data, or manually reinstalling programs and copying over your data. (The Mac OS X 10.2 installer actually included an Archive And Install option, which preserved your original OS in a special folder while installing a completely new, fresh copy of 10.3. This feature was eliminated in the Snow Leopard OS X 10.6 installer.)
But a new download-and-install procedure debuted with Lion (OS X 10.7) and continued through Mountain Lion (OS X 10.8) and now Mavericks (OS X 10.9). Instead of a bootable installation DVD, you download the latest OS X installer to your Mac and install the new OS from the same drive. With the debut of Mavericks, as with Mountain Lion and Lion, many Mac users are asking two related questions: (1) Can you perform a clean install of Mavericks? and (2) Should you? Here's my take on each of these questions, which is essentially the same as with Mountain Lion last year.
Can you perform a clean install of Mavericks?
First, the technical question: Given that the OS X 10.9 installer doesn't include an official clean-install option, is it possible to perform such an installation? The simple answer is: Yes. As explained in my main article on installing Mavericks, the installer will let you install the new OS onto a blank drive. So if you first back up your existing Mountain Lion, Lion, or Snow Leopard (OS X 10.6) installation and all your files--I recommend creating a bootable clone using SuperDuper or Carbon Copy Cloner--you can then boot from a bootable installer drive, erase your Mac's normal startup drive, and install Mavericks on it. In fact, you can use the instructions in my article on how to install Mavericks over Leopard. Specifically, scroll down to the section called "The brute-force method" and perform Steps 1 through 7, substituting "Mountain Lion," "Lion," or "Snow Leopard" for "Leopard"--the result is a clean install.
Once you've done this, if you want to use Setup/Migration Assistant to restore data from your backup, proceed with Step 8. If you truly want a clean start, you'll instead need to manually copy your personal data from your backup to your new Mavericks installation, and then reinstall all of your software. (This is one situation in which the more apps you've purchased through the Mac App Store, the better--you just launch the Mac App Store app and click a few buttons to automatically reinstall everything you've purchased.)
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.)