Cannot "brew update" anymore - fails to git pull formulas

[MPV]

EDIT: The TLDR solution:

cd `brew --prefix`
git remote add origin https://github.com/mxcl/homebrew.git
git fetch origin
git reset --hard origin/master

The story behind it:

Hi, Recently I started getting this output when I run "brew update". I can't recall having done anything special that would affect my homebrew installation.

$ brew update
error: Your local changes to the following files would be overwritten by merge:
    Library/Aliases/bjam
    Library/Aliases/gpg2
    Library/Contributions/brew_bash_completion.sh
    Library/Contributions/manpages/brew.1.md
    Library/Formula/a2ps.rb
    Library/Formula/aalib.rb
    Library/Formula/abcde.rb
    Library/Formula/abiword.rb
    Library/Formula/abook.rb
    Library/Formula/abuse.rb
    Library/Formula/ace.rb
    Library/Formula/ack.rb
    Library/Formula/activemq.rb
    Library/Formula/adobe-air-sdk.rb
    Library/Formula/advancecomp.rb
    Library/Formula/aescrypt.rb
    Library/Formula/afsctool.rb
    Library/Formula/aften.rb
    Library/Formula/aget.rb
    Library/Formula/aggregate.rb
    Library/Formula/agrep.rb
    Library/Formula/aircrack-ng.rb
    Library/Formula/aldo.rb
    Library/Formula/algol68g.rb
    Library/Formula/alpine.rb
    Library/Formula/amap.rb
    Library/Formula/android-sdk.rb
    Library/Formula/ann.rb
    Library/Formula/ansifilter.rb
    Library/Formula/antiword.rb
    Library/Formula/antlr.rb
    Library/Formula/anttweakbar.rb
    Library/Formula/aoeui.rb
    Library/Formula/apg.rb
    Library/Formula/apgdiff.rb
    Library/Formula/apiextractor.rb
    Library/Formula/apktool.rb
    Library/Formula/aplus.rb
    Library/Formula/app-engine-java-sdk.rb
    Library/Formula/apt-dater.rb
    Library/Formula/aqbanking.rb
    Library/Formula/arabica.rb
    Library/Formula/aria2.rb
    Library/Formula/arm.rb
    Library/Formula/armadillo.rb
    Library/Formula/arping.rb
    Library/Formula/arss.rb
    Library/Formula/assimp.rb
    Library/Formula/astyle.rb
    Library/Formula/asymptote.rb
    Library/Formula/aterm.rb
    Library/Formula/atk.rb
    Library/Formula/atlassian-plugin-sdk.rb
    Library/Formula/atomicparsley.rb
    Library/Formula/atool.rb
    Library/Formula/auctex.rb
    Library/Formula/audiofile.rb
    Library/Formula/authexec.rb
    Library/Formula/auto-scaling.rb
    Library/Formula/autobench.rb
    Library/Formula/autogen.rb
    Library/Formula/automoc4.rb
    Library/Formula/autossh.rb
    Library/Formula/aview.rb
    Library/Formula/avra.rb
    Library/Formula/avro-c.rb
    Library/Formula/aws-cfn-tools.rb
    Library/Formula/aws-elasticache.rb
    Library/Formula/aws-iam-tools.rb
    Library/Formula/babl.rb
    Library/Formula/bagit.rb
    Library/Formula/bali-phy.rb
    Library/Formula/bash-completion.rb
    Library/Formula/bazaar.rb
    Library/Formula/bbcp.rb
    Library/Formula/bcrypt.rb
    Library/Formula/bcwipe.rb
    Library/Formula/bdw-gc.rb
    Library/Formula/beanstalk.rb
    Library/Formula/bedtools.rb
    Library/Formula/berkeley-db.rb
    Library/Formula/bibutils.rb
    Library/Formula/binutils.rb
    Library/Formula/binwalk.rb
    Library/Formula/bitlbee.rb
    Library/Formula/blahtexml.rb
    Library/Formula/blast.rb
    Library/Formula/blitz.rb
    Library/Formula/blueutil.rb
    Library/Formula/boost.rb
    Library/Formula/botan.rb
    Library/Formula/box2d.rb
    Library/Formula/boxes.rb
    Library/Formula/bsdiff.rb
    Library/Formula/bulk_extractor.rb
    Library/Formula/bwa.rb
    Library/Formula/bwm-ng.rb
    Library/Formula/byobu.rb
    Library/Formula/c10t.rb
    Library/Formula/cabal-install.rb
    Library/Formula/cadaver.rb
    Library/Formula/cairo.rb
    Library/Formula/cairomm.rb
    Library/Formula/calabash.rb
    Library/Formula/cantera.rb
    Library/Formula/cassandra.rb
    Library/Formula/cc65.rb
    Library/Formula/cdargs.rb
    Library/Formula/cdecl.rb
    Library/Formula/cdrdao.rb
    Library/Formula/ceylon.rb
    Library/Formula/cfengine.rb
    Library/Formula/cfitsio.rb
    Library/Formula/cgal.rb
    Library/Formula/cgdb.rb
    Library/Formula/cheops.rb
    Library/Formula/chibi-scheme.rb
    Library/Formula/chipmunk.rb
    Library/Formula/chkrootkit.rb
    Library/Formula/chromaprint.rb
    Library/Formula/cimg.rb
    Library/Formula/clay.rb
    Library/Formula/clisp.rb
    Library/Formula/cloc.rb
    Library/Formula/closure-compiler.rb
    Library/Formula/cloud-watch.rb
    Library/Formula/cloudbees-sdk.rb
    Library/Formula/clozure-cl.rb
    Library/Formula/clucene.rb
    Library/Formula/clusterit.rb
    Library/Formula/clutter.rb
    Library/Formula/cmake.rb
    Library/Formula/cmigemo.rb
    Library/Formula/cminpack.rb
    Library/Formula/cmu-pocketsphinx.rb
    Library/Formula/cmu-sphinxbase.rb
    Library/Formula/cmucl.rb
    Library/Formula/cmus.rb
    Library/Formula/coffee-script.rb
    Library/Formula/collectd.rb
    Library/Formula/co
error: The following untracked working tree files would be overwritten by merge:
    Library/Aliases/boost-jam
    Library/Aliases/fastcgi
    Library/Aliases/nodejs
    Library/Aliases/pocketsphinx
    Library/Aliases/sphinxbase
    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-switch.rb
    Library/Contributions/cmds/brew-unpack.rb
    Library/Contributions/cmds/brew-which.rb
    Library/Contributions/install_homebrew.rb
    Library/Formula/abcl.rb
    Library/Formula/ape.rb
    Library/Formula/apollo.rb
    Library/Formula/appledoc.rb
    Library/Formula/arp-scan.rb
    Library/Formula/atkmm.rb
    Library/Formula/autoconf.rb
    Library/Formula/autoenv.rb
    Library/Formula/autojump.rb
    Library/Formula/automake.rb
    Library/Formula/avocadodb.rb
    Library/Formula/blackbox.rb
    Library/Formula/boost-build.rb
    Library/Formula/bro.rb
    Library/Formula/bsdmake.rb
    Library/Formula/cbmbasic.rb
    Library/Formula/cloog.rb
    Library/Formula/conserver.rb
    Library/Formula/crush-tools.rb
    Library/Formula/dart.rb
    Library/Formula/di.rb
    Library/Formula/dsniff.rb
    Library/Formula/dupx.rb
    Library/Formula/echoping.rb
    Library/Formula/ecm.rb
    Library/Formula/eprover.rb
    Library/Formula/ext2fuse.rb
    Library/Formula/ezlupdate.rb
    Library/Formula/f3.rb
    Library/Formula/fasd.rb
    Library/Formula/fceux.rb
    Library/Formula/fcgi.rb
    Library/Formula/findbugs.rb
    Library/Formula/freerdp.rb
    Library/Formula/funcoeszz.rb
    Library/Formula/gabedit.rb
    Library/Formula/gibbslda.rb
    Library/Formula/git-diffall.rb
    Library/Formula/git-ftp.rb
    Library/Formula/gnu-arch.rb
    Library/Formula/gnumeric.rb
    Library/Formula/gnunet.rb
    Library/Formula/go-app-engine-32.rb
    Library/Formula/go-app-engine-64.rb
    Library/Formula/goffice.rb
    Library/Formula/grace.rb
    Library/Formula/grib-api.rb
    Library/Formula/griffon.rb
    Library/Formula/gtk-doc.rb
    Library/Formula/gtmess.rb
    Library/Formula/hg-flow.rb
    Library/Formula/hqx.rb
    Library/Formula/imap-uw.rb
    Library/Formula/ispell.rb
    Library/Formula/ivy.rb
    Library/Formula/jing.rb
    Library/Formula/knife-completion.rb
    Library/Formula/konoha.rb
    Library/Formula/libcouchbase.rb
    Library/Formula/libcuefile.rb
    Library/Formula/libextractor.rb
    Library/Formula/libgaiagraphics.rb
    Library/Formula/libgnomecanvas.rb
    Library/Formula/libkate.rb
    Library/Formula/libqalculate.rb
    Library/Formula/libreplaygain.rb
    Library/Formula/libtool.rb
    Library/Formula/libvbucket.rb
    Library/Formula/lifelines.rb
    Library/Formula/mdxmini.rb
    Library/Formula/meld.rb
    Library/Formula/minuit2.rb
    Library/Formula/mobile-shell.rb
    Library/Formula/monetdb.rb
    Library/Formula/mp3info.rb
    Library/Formula/mpio.rb
    Library/Formula/msgpack-rpc.rb
    Library/Formula/musepack.rb
    Library/Formula/nacl.rb
    Library/Formula/nauty.rb
    Library/Formula/nrpe.rb
    Library/Formula/num-utils.rb
    Library/Formula/oath-toolkit.rb
    Library/Formula/open-babel.rb
    Library/Formula/orbit.rb
    Library/Formula/par2tbb.rb
    Library/Formula/pcb.rb
    Library/Formula/pdksh.rb
    Library/Formula/perforce-proxy.rb
    Library/Formula/pgdbf.rb
    Library/Formula/phyml.rb
    Library/Formula/pmdmini.rb
    Library/Formula/primesieve.rb
    Library/Formula/pulledpork.rb
    Library/Formula/py2cairo.rb
    Library/Formula/pygobject.rb
    Library/Formula/pygtk.rb
    Library/Formula/quickfix.rb
    Library/Formula/rarian.rb
    Library/Formula/rc.rb
    Library/Formula/riemann.rb
    Library/Formula/rsense.rb
    Library/Formula/sam2p.rb
    Library/Formula/savana.rb
    Library/Formula/sdl_rtf.rb
    Library/Formula/selenium-server-standalone.rb
    Library/Formula/skytools.rb
    Library/Formula/sonar.rb
    Library/Formula/tcpurify.rb
    Library/Formula/the_silver_searcher.rb
    Library/Formula/tkdiff.rb
    Library/Formula/trang.rb
    Librar
Aborting
Error: Failure while executing: git pull -q origin refs/heads/master:refs/remotes/origin/master

[davidrinnan]

@MPV saved my day

[mschipperheyn]

perfect

[jesse-wang]

@MPV worked for me

[AndyBean]

Thanks for the fix. I needed it even today on OSX 10.9. I even had to sudo the last command too, sudo git reset --hard origin/master

[MikeMcQuaid]

If you had to use sudo instead I recommend running before that: sudo chown -R $USER /usr/local

[tigris]

Whilst this solution was awesome and worked for me too, I can't help but wonder how my homebrew got into modified state in the first place. I certainly didn't make the changes git status seemed to think I made.

[grayghostvisuals]

Longest. Running. Issue. Thread. Ever.

[johnnygoodman]

@MPV thanks!