Regarding your app corruption, docset bug, filesystem corruption and general filesystem slowness, are you sure you don't have a bad SSD/HD or bad RAM?
- App Store likely has a problem with storeaccountd / installer framework from the exception traces I've seen (debug menu on).
- HFS+ can corrupt itself irreparably (it's not ZFS). BTDTBTTS.
Apple introduced a new virtualisation framework in Yosemite, hence the rereleases of the most widely used virtualization items (Parallels and Fusion).