I ran DiskWarrior prior to the installation of Yosemite and my directory was under 3% fragmented. Post installation of Yosemite, it was 46%. My friend's was similar at 43%. Since rebuilding the directory, I've noticed a reduction in lag, which seems to be a particular problem with Yosemite and integrated graphics cards (My discrete Nvidia works well, but the HD4000 is not a fan). Anyone else with a similar experience re: directories?