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If you can't boot into Safe mode (I couldn't on a rMBP with 10.8.3), you can perform the following sequence to make it boot to Safe mode (source https://discussions.apple.com/message/21366643#21366643):

  cd /sbin
  sudo mv fsck_hfs fsck_hfs_orig
  sudo cp -p /usr/bin/true fsck_hfs
  nvram boot-args="-x -v"
  
  reboot, log in
  
  sudo nvram boot-args=""
   
  reboot
   
  cd /sbin
  sudo mv fsck_hfs_orig fsck_hfs


Why are you moving fsck_hfs around? I do notice if i'm booting into safe mode that fsck_hfs is taking FOREVER. (running 12 hours so far on my retina mbp 15, which is ludicrous)

But just switching to single user (aka boot-args="-s -v") and manually running fsck_hfs -c 4096m -f -d /dev/disk1 (or equivalent) I managed to clean up / of a few problems in under 4 minutes. fsck_hfs looks like it could use some fixing to dynamically cache things better, that or they could give it default arguments based on the systems memory size to speed things along.

Either way I'm done with trying to fix this, just going to reinstall 10.8.3 from scratch and rsync over my home directory and reinstall vmware. I've tried about every fix for the sandbox nonsense, and since this system had 10.7 originally maybe it upgraded badly, whatever.




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