homebrew brew doctor fail message

Question

I am going through my home brew doctor messages and no matter what I do I can not seem to remove this message:

Warning: You have uncommitted modifications to Homebrew's core.

Unless you know what you are doing, you should run: cd /usr/local && git reset --hard

Does anyone have any idea on how to get rid of this?

From git status /usr/local

#   Library/Aliases/dwarffortress
#   Library/Aliases/ultima4
#   Library/Aliases/ultima7
#   Library/Contributions/examples/
#   Library/Formula/abfind.rb
#   Library/Formula/abuse.rb
#   Library/Formula/akonadi.rb
#   Library/Formula/angband.rb
#   Library/Formula/apc.rb
#   Library/Formula/aqua-less.rb
#   Library/Formula/argp-standalone.rb
#   Library/Formula/attica.rb
#   Library/Formula/bashreduce.rb
#   Library/Formula/c10t.rb
#   Library/Formula/chocolate-doom.rb
#   Library/Formula/cmigemo.rb
#   Library/Formula/coffee-script.rb
#   Library/Formula/csstidy.rb
#   Library/Formula/dosbox.rb
#   Library/Formula/dotless.rb
#   Library/Formula/dwarf-fortress.rb
#   Library/Formula/exult.rb
#   Library/Formula/flip.rb
#   Library/Formula/frobtads.rb
#   Library/Formula/frotz.rb
#   Library/Formula/gearman-php.rb
#   Library/Formula/gnu-chess.rb
#   Library/Formula/gnu-go.rb
#   Library/Formula/growlme.rb
#   Library/Formula/imagick.rb
#   Library/Formula/inform6.rb
#   Library/Formula/jnethack.rb
#   Library/Formula/jwhois.rb
#   Library/Formula/kde-phonon.rb
#   Library/Formula/kdebase-runtime.rb
#   Library/Formula/kdelibs.rb
#   Library/Formula/kdepimlibs.rb
#   Library/Formula/libgdiplus.rb
#   Library/Formula/libiconv.rb
#   Library/Formula/libsgml.rb
#   Library/Formula/maatkit.rb
#   Library/Formula/mcrypt-php.rb
#   Library/Formula/mednafen.rb
#   Library/Formula/memcache-php.rb
#   Library/Formula/memcached-php.rb
#   Library/Formula/memcachedb.rb
#   Library/Formula/midgard2-php.rb
#   Library/Formula/mongo-php.rb
#   Library/Formula/n2n.rb
#   Library/Formula/nazghul.rb
#   Library/Formula/nethack.rb
#   Library/Formula/netris.rb
#   Library/Formula/ninja.rb
#   Library/Formula/open-tyrian.rb
#   Library/Formula/orderly.rb
#   Library/Formula/oxygen-icons.rb
#   Library/Formula/parsley.rb
#   Library/Formula/pbrt.rb
#   Library/Formula/pcntl-php.rb
#   Library/Formula/phpmyadmin.rb
#   Library/Formula/pioneers.rb
#   Library/Formula/platypus.rb
#   Library/Formula/pspell-php.rb
#   Library/Formula/qimageblitz.rb
#   Library/Formula/robotfindskitten.rb
#   Library/Formula/shared-desktop-ontologies.rb
#   Library/Formula/shen.rb
#   Library/Formula/slashem.rb
#   Library/Formula/solr-php.rb
#   Library/Formula/soprano.rb
#   Library/Formula/sparse.rb
#   Library/Formula/spim.rb
#   Library/Formula/stone-soup.rb
#   Library/Formula/strigi.rb
#   Library/Formula/uggconv.rb
#   Library/Formula/unnethack.rb
#   Library/Formula/voldemort.rb
#   Library/Formula/woof.rb
#   Library/Formula/xboard.rb
#   Library/Formula/xcache.rb
#   Library/Formula/xdebug.rb
#   Library/Formula/xmoto.rb
#   Library/Formula/xu4.rb
#   Library/Homebrew/test/tests

Answer 1

After posting on the homebrew issues log https://github.com/mxcl/homebrew/issues/11761 I was able to clear the error by running git clean -df and once that is finished brew doctor. Once complete you should see:

Your system is raring to brew.