There is no "clean install" for OS X.
OS X Installation types.
1. Install "over the top" - either an upgrade from 10.x to 10.(x+1), or installing the same exact version.
2. "Archive Install" - moves the old System and Library and OSX-supplied Applications to "Previous Systems".
3. "Erase and Install" - backup first! This erases your drive completely, and installs OS X. You then need to restore your data from backup, and reinstall 3rd party apps.
Method #2 is the closest in function to OS 9's old "clean install", which moved "System Folder" into "Previous System". However, #3 is what most people seem to refer to when suggesting a "clean install" of OS X. Because of this ambiguity, and the resultant difficulty distinguishing between the least destructive and most destructive OS X install options, either one of which someone may mean when referring to a "clean install", I never actually recommend a clean install, but either an archive or an erase. Note that there are no Apple documents recommending a "clean install" for OS X - also due to this .
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