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

Go to that folder [first command] which also should update permissions (if not see below)
Fetch the origin [second command] which means to update your LOCAL version of the remote branch of brew
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:

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

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

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