Update: As several of our commenters pointed out, the OS is probably running the fsck utility in the background to repair directory problems, while showing the progress bar to the end user so they know there's something going on (fsck can take quite a while). Here's an older Apple support article...
You may sincerely wish never to need it, but if you run into a situation where your Mac refuses to boot fully to the Finder and you don't have any boot-capable utilities to tackle the problem, Kristofer Widholm's AppleJack is probably your best friend in the trenches. The single-user-mode tool is...
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