Why are all my Homebrew packages suddenly "disconnected"; how can i fix this?

Question

Recently, a brew doctor or brew upgrade --all (I'm not sure I ran them in a script), reporting the following:

 Homebrew from 5371359 to e3fe270. Updated 3 taps (caskroom/cask, homebrew/boneyard, homebrew/core). Error: Could not symlink bin/dvipdf Target /usr/local/bin/dvipdf already exists. You may want to remove it: rm '/usr/local/bin/dvipdf' To force the link and overwrite all conflicting files: brew link --overwrite ghostscript To list all files that would be deleted: brew link --overwrite --dry-run ghostscript Error: Could not symlink bin/easy_install Target /usr/local/bin/easy_install already exists. You may want to remove it: rm '/usr/local/bin/easy_install' To force the link and overwrite all conflicting files: brew link --overwrite python To list all files that would be deleted: brew link --overwrite --dry-run python: 

I followed these instructions by doing:

  brew link --overwrite python brew link --overwrite ghostscript 

But now when I run brew doctor get:

 Warning: You have unlinked kegs in your Cellar Leaving kegs unlinked can lead to build-trouble and cause brews that depend on those kegs to fail to run properly once built. Run `brew link` on these: # A list of EVERYTHING listed by brew list 

That is: brew doctor now shows everything that I installed - everything listed in the brew list - as unrelated!

What's going on here? Why has everything I ever installed using Homebrew turned off unexpectedly? How did they do that? What can I (safely) do to fix my Homebrew installation (other than manually running brew link --overwrite ... individually for each thing I installed?

Answer 1

Running brew update (twice if necessary) should sort it.

If not, brew unlink $(brew list); brew link $(brew list) brew unlink $(brew list); brew link $(brew list) will be.