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As pointed out by @Sydmanhere, Google released the factory images for the Nexus 6 updating it to LMY47E. Being the difference is just one letter the update is likely a minor one. If you want to grab the latest update you can head over to Google's website and manually install it through fastboot.
I'm running MeanPop which is stock with a few tweaks by MikeyXda.. But there is also a deodex stock file ROM which is off OTA.... Also CleanRom will be coming in a few days which is also stock...