I've been trying to solve the issue seen here:
The recommended solution is to do a safe boot which clears various caches etc, however I'm unable to complete a safe boot. It gets stuck with the progress bar only about 5% complete; I even tried leaving the machine on overnight, about 8-9 hours.
I also tried safe booting via rEFInd which gets rid of the apple logo and lets me see what's actually happening and it's getting stuck on the 'fsck_hfs -r' step 'checking catalog file.' I ran this command manually from recovery mode on the same disk and it completed just fine in 15-20min but safe boot still gets stuck. I've also tried clearing PRAM in case that helps any.
Any other ideas for getting into safe mode? Is it possible to run the safe boot 'script' manually from recovery mode? Does such a script exist?