brew update: The following untracked working tree files would be overwritten by merge:

I tried to run brew update and I get an error about my local changes would be lost if I merged. I tried committing my local changes (don't remember making any, but it's been awhile), and that made things worse.

Here's the output:

MBP:Library User$ sudo brew update
error: The following untracked working tree files would be overwritten by merge:
	Library/Aliases/fastcgi
	Library/Aliases/htop
	Library/Aliases/nodejs
	Library/Aliases/ocio
	Library/Aliases/oiio
	Library/Aliases/pgrep
	Library/Aliases/pkill
	Library/Contributions/cmds/brew-beer.rb
	Library/Contributions/cmds/brew-dirty.rb
	Library/Contributions/cmds/brew-graph
	Library/Contributions/cmds/brew-grep
	Library/Contributions/cmds/brew-leaves.rb
	Library/Contributions/cmds/brew-linkapps.rb
	Library/Contributions/cmds/brew-man
	Library/Contributions/cmds/brew-mirror-check.rb
	Library/Contributions/cmds/brew-missing.rb
	Library/Contributions/cmds/brew-pull.rb
	Library/Contributions/cmds/brew-readall.rb
	Library/Contributions/cmds/brew-server
	Library/Contributions/cmds/brew-services.rb
	Library/Contributions/cmds/brew-switch.rb
	Library/Contributions/cmds/brew-test-bot.commit.html.erb
	Library/Contributions/cmds/brew-test-bot.css
	Library/Contributions/cmds/brew-test-bot.index.html.erb
	Library/Contributions/cmds/brew-test-bot.rb
	Library/Contributions/cmds/brew-tests.rb
	Library/Contributions/cmds/brew-unpack.rb
	Library/Contributions/cmds/brew-which.rb
	Library/Contributions/install_homebrew.rb
	Library/Formula/abcl.rb
	Library/Formula/abyss.rb
	Library/Formula/akka.rb
	Library/Formula/apollo.rb
	Library/Formula/appledoc.rb
	Library/Formula/arangodb.rb
	Library/Formula/autoconf.rb
	Library/Formula/automake.rb
	Library/Formula/avidemux.rb
	Library/Formula/bind.rb
	Library/Formula/bsdconv.rb
	Library/Formula/bsdmake.rb
	Library/Formula/camellia.rb
	Library/Formula/cbmbasic.rb
	Library/Formula/cdo.rb
	Library/Formula/checkstyle.rb
	Library/Formula/cifer.rb
	Library/Formula/clhep.rb
	Library/Formula/collada-dom.rb
	Library/Formula/crash.rb
	Library/Formula/crossroads.rb
	Library/Formula/css-crush.rb
	Library/Formula/curlftpfs.rb
	Library/Formula/dart.rb
	Library/Formula/dasm.rb
	Library/Formula/dfc.rb
	Library/Formula/di.rb
	Library/Formula/dsniff.rb
	Library/Formula/dupx.rb
	Library/Formula/dwatch.rb
	Library/Formula/eprover.rb
	Library/Formula/ext2fuse.rb
	Library/Formula/ezlupdate.rb
	Library/Formula/f3.rb
	Library/Formula/fastx_toolkit.rb
	Library/Formula/fceux.rb
	Library/Formula/findbugs.rb
	Library/Formula/freerdp.rb
	Library/Formula/funcoeszz.rb
	Library/Formula/fwknop.rb
	Library/Formula/gabedit.rb
	Library/Formula/gbdfed.rb
	Library/Formula/gconf.rb
	Library/Formula/git-encrypt.rb
	Library/Formula/glm.rb
	Library/Formula/gmap-gsnap.rb
	Library/Formula/gnu-arch.rb
	Library/Formula/gnunet.rb
	Library/Formula/gobby.rb
	Library/Formula/gptfdisk.rb
	Library/Formula/griffon.rb
	Library/Formula/grok.rb
	Library/Formula/gtk-chtheme.rb
	Library/Formula/gtkglextmm.rb
	Library/Formula/gtmess.rb
	Library/Formula/hg-flow.rb
	Library/Formula/hqx.rb
	Library/Formula/htop-osx.rb
	Library/Formula/htpdate.rb
	Library/Formula/imap-uw.rb
	Library/Formula/iozone.rb
	Library/Formula/ipbt.rb
	Library/Formula/ipe.rb
	Library/Formula/ispc.rb
	Library/Formula/ispell.rb
	Library/Formula/jigdo.rb
	Library/Formula/jing.rb
	Library/Formula/jless.rb
	Library/Formula/jpeginfo.rb
	Library/Formula/konoha.rb
	Library/Formula/legit.rb
	Library/Formula/libcouchbase.rb
	Library/Formula/libcuefile.rb
	Library/Formula/libextractor.rb
	Library/Formula/libglademm.rb
	Library/Formula/libgtextutils.rb
	Library/Formula/libinfinity.rb
	Library/Formula/libkate.rb
	Library/Formula/libqalculate.rb
	Library/Formula/libqglviewer.rb
	Library/Formula/libreplaygain.rb
	Library/Formula/libtool.rb
	Library/Formula/libvbucket.rb
	Library/Formula/libvo-aacenc.rb
	Library/Formula/libxmi.rb
	Library/Formula/lifelines.rb
	Library/Formula/makeicns.rb
	Library/Formula/mathgl.rb
	Library/Formula/meld.rb
	Library/Formula/mesalib-glw.rb
	Library/Formula/minisat.rb
	Library/Formula/minuit2.rb
	Library/Formula/mobile-shell.rb
	Library/Formula/movgrab.rb
	Library/Formula/mp3cat.rb
	Library/Formula/mpich2.rb
	Library/Formula/mrfast.rb
	Library/Formula/musepack.rb
	Library/Formula/ndiff.rb
	Library/Formula/net6.rb
	Library/Formula/nrpe.rb
	Library/Formula/nuttcp.rb
	Library/Formula/oath-toolkit.
Updating aa07533..3f070ef
Aborting
Error: Failed while executing git pull  origin refs/heads/master:refs/remotes/origin/master

Don't forget to fetch the origin:

cd /usr/local/Homebrew
git fetch origin
git reset --hard origin/master

What happens is that you are trying to update brew, but brew itself is either not up to date (likely), there is a permissions change via some OS update (also likely), or brew is slightly corrupt (unlikely). Since brew itself is a git repo, you have to update or reset brew to the master branch version. brew [by default] is located in the /usr/local/Homebrew folder, so you

1. Go to that folder [first command] which also should update permissions (if not see below)
2. Fetch the origin [second command] which means to update your LOCAL version of the remote branch of brew
3. Hard reset [3rd command] based on the REMOTE master branch (which also uses your current permissions).

You can also chown the first command if you are in a non sudo or admin profile

sudo chown -R `whoami` /usr/local/Homebrew
cd /usr/local/Homebrew
git reset --hard origin/master

To understand git reset, take a look at this article.

I had a similar issue a couple weeks ago trying to update an old homebrew install. Doing this:

git reset --hard origin/master

in /usr/local fixed it for me.

It seems like other folks have had this issue too. Have you looked over any of the proposed workarounds here?

I'm adding my personal experience, since it seems a little safer than what proposed in 2012:

1. Run brew doctor.

2. If you get the following warning:

   Warning: The /usr/local directory is not writable.
   

   run:

   sudo chown -R `whoami` /usr/local
   

   to fix the permissions problems (as suggested also by Chris Frisina). Eventually run brew doctor again to ensure yourself that the warning is gone.

3. Now, you should have a

   Warning: You have uncommitted modifications to Homebrew
   

   that may bey solved by

   cd /usr/local/Library && git stash && git clean -d -f
   

as suggested by Dr.Brew itself. The command stashes the uncommitted modifications so you could go back and recover them if needed. It seemed safer than git reset --hard origin/master to me.

4. If you wish, check the official troubleshooting guide if the steps suggested here and by other SO users does not solve your problem.

Similar answer but if you have files that are no longer tracked you need additional step so from /usr/local run

git fetch origin
git clean -f
git reset --hard origin/master

This approach may be simpler than some. It involves:

• fixing a git issue so you can delegate management of changes to it again.
• no manual moves of files or directories.
• no manual adjustments of file or directory permissions.

Steps (with notes for those who want explanations):

cd $(brew --repository)                              // see Note 1 below
git remote add brew https://github.com/Homebrew/brew // see Note 2 below
git pull brew master                                 // promising fast-forward report!
brew update                                          // see Note 3 below 

Overview:
From what I can tell, the actual cause of this issue is a change in the repo url. It's now brew and was brew.git. (Full up-to-date url: https://github.com/Homebrew/brew)

Note 1: This first command takes you from anywhere in your file structure to the correct directory. The directory structure is different for me than what others show above (Mac OS 10.11.16), but with this command, those differences should not matter.

Note 2: This second command adds the correct remote url to a new alias; I did so just in case this approach didn't accomplish what I wanted and I needed the previous address again. Since the new remote worked, I'll invite someone else to comment on simply changing the url aliased by origin. I'll happily update the answer to reflect what worked for you.

Note 3: This forth command has exactly the desired result: it reports a large number of updates, including the particularly nice report of "==> Migrated HOMEBREW_REPOSITORY to /usr/local/Homebrew!" (emphasis theirs).