diff --git a/Library/Homebrew/cmd/update-report.rb b/Library/Homebrew/cmd/update-report.rb
index c068d02eef..fa82c875d4 100644
--- a/Library/Homebrew/cmd/update-report.rb
+++ b/Library/Homebrew/cmd/update-report.rb
@@ -75,6 +75,7 @@ module Homebrew
     end
 
     migrate_legacy_cache_if_necessary
+    migrate_legacy_keg_symlinks_if_necessary
 
     if !updated
       if !ARGV.include?("--preinstall") && !ENV["HOMEBREW_UPDATE_FAILED"]
@@ -167,6 +168,24 @@ module Homebrew
     end
   end
 
+  def migrate_legacy_keg_symlinks_if_necessary
+    legacy_linked_kegs = HOMEBREW_LIBRARY/"LinkedKegs"
+    return unless legacy_linked_kegs.directory?
+
+    legacy_linked_kegs.children.each {|f| Keg.new(f.realpath).link }
+    FileUtils.rm_rf legacy_linked_kegs
+
+    legacy_pinned_kegs = HOMEBREW_LIBRARY/"PinnedKegs"
+    return unless legacy_pinned_kegs.directory?
+
+    legacy_pinned_kegs.children.each do |f|
+      pin_version = Keg.new(f.realpath).version
+      formula = Formulary.factory(f.basename.to_s)
+      FormulaPin.new(formula).pin_at(pin_version)
+    end
+    FileUtils.rm_rf legacy_pinned_kegs
+  end
+
   def link_completions_and_docs
     return if HOMEBREW_PREFIX.to_s == HOMEBREW_REPOSITORY.to_s
     command = "brew update"
diff --git a/Library/Homebrew/config.rb b/Library/Homebrew/config.rb
index cef6153654..19ad7a7e54 100644
--- a/Library/Homebrew/config.rb
+++ b/Library/Homebrew/config.rb
@@ -17,8 +17,14 @@ HOMEBREW_LIBRARY = Pathname.new(ENV["HOMEBREW_LIBRARY"])
 # Where shim scripts for various build and SCM tools are stored
 HOMEBREW_SHIMS_PATH = HOMEBREW_LIBRARY/"Homebrew/shims"
 
+# Where we store symlinks to currently linked kegs
+HOMEBREW_LINKED_KEGS = HOMEBREW_PREFIX/"var/homebrew/linked"
+
+# Wehere we store symlinks to currently version-pinned kegs
+HOMEBREW_PINNED_KEGS = HOMEBREW_PREFIX/"var/homebrew/pinned"
+
 # Where we store lock files
-HOMEBREW_LOCK_DIR = HOMEBREW_LIBRARY/"Locks"
+HOMEBREW_LOCK_DIR = HOMEBREW_PREFIX/"var/homebrew/locks"
 
 # Where we store built products
 HOMEBREW_CELLAR = Pathname.new(ENV["HOMEBREW_CELLAR"])
diff --git a/Library/Homebrew/global.rb b/Library/Homebrew/global.rb
index 36eb97baaa..8472eba5cb 100644
--- a/Library/Homebrew/global.rb
+++ b/Library/Homebrew/global.rb
@@ -22,9 +22,6 @@ require "config"
 
 HOMEBREW_REPOSITORY.extend(GitRepositoryExtension)
 
-HOMEBREW_LINKED_KEGS = HOMEBREW_LIBRARY/"LinkedKegs"
-HOMEBREW_PINNED_KEGS = HOMEBREW_LIBRARY/"PinnedKegs"
-
 RUBY_PATH = Pathname.new(RbConfig.ruby)
 RUBY_BIN = RUBY_PATH.dirname
 
diff --git a/Library/Homebrew/keg.rb b/Library/Homebrew/keg.rb
index 68a96024fe..febb60971b 100644
--- a/Library/Homebrew/keg.rb
+++ b/Library/Homebrew/keg.rb
@@ -66,7 +66,7 @@ class Keg
   INFOFILE_RX = %r{info/([^.].*?\.info|dir)$}
   TOP_LEVEL_DIRECTORIES = %w[bin etc include lib sbin share var Frameworks]
   ALL_TOP_LEVEL_DIRECTORIES = (TOP_LEVEL_DIRECTORIES + %w[lib/pkgconfig share/locale share/man opt]).freeze
-  PRUNEABLE_DIRECTORIES = %w[bin etc include lib sbin share Frameworks LinkedKegs].map do |d|
+  PRUNEABLE_DIRECTORIES = %w[bin etc include lib sbin share Frameworks LinkedKegs var/homebrew].map do |d|
     case d when "LinkedKegs" then HOMEBREW_LIBRARY/d else HOMEBREW_PREFIX/d end
   end
 
diff --git a/Library/Homebrew/test/lib/config.rb b/Library/Homebrew/test/lib/config.rb
index 713bc9c3a4..98144d71e1 100644
--- a/Library/Homebrew/test/lib/config.rb
+++ b/Library/Homebrew/test/lib/config.rb
@@ -24,6 +24,8 @@ HOMEBREW_REPOSITORY    = HOMEBREW_PREFIX
 HOMEBREW_LIBRARY       = HOMEBREW_REPOSITORY+"Library"
 HOMEBREW_CACHE         = HOMEBREW_PREFIX.parent+"cache"
 HOMEBREW_CACHE_FORMULA = HOMEBREW_PREFIX.parent+"formula_cache"
+HOMEBREW_LINKED_KEGS   = HOMEBREW_PREFIX.parent+"linked"
+HOMEBREW_PINNED_KEGS   = HOMEBREW_PREFIX.parent+"pinned"
 HOMEBREW_LOCK_DIR      = HOMEBREW_PREFIX.parent+"locks"
 HOMEBREW_CELLAR        = HOMEBREW_PREFIX.parent+"cellar"
 HOMEBREW_LOGS          = HOMEBREW_PREFIX.parent+"logs"
diff --git a/Library/Homebrew/test/test_integration_cmds.rb b/Library/Homebrew/test/test_integration_cmds.rb
index 5b64dfd85b..3eef415154 100644
--- a/Library/Homebrew/test/test_integration_cmds.rb
+++ b/Library/Homebrew/test/test_integration_cmds.rb
@@ -14,6 +14,8 @@ class IntegrationCommandTests < Homebrew::TestCase
   def teardown
     coretap = CoreTap.new
     paths_to_delete = [
+      HOMEBREW_LINKED_KEGS,
+      HOMEBREW_PINNED_KEGS,
       HOMEBREW_CELLAR.children,
       HOMEBREW_CACHE.children,
       HOMEBREW_LOCK_DIR.children,
@@ -22,7 +24,6 @@ class IntegrationCommandTests < Homebrew::TestCase
       HOMEBREW_PREFIX/"bin",
       HOMEBREW_PREFIX/"share",
       HOMEBREW_PREFIX/"opt",
-      HOMEBREW_LINKED_KEGS,
       HOMEBREW_LIBRARY/"Taps/caskroom",
       HOMEBREW_LIBRARY/"Taps/homebrew/homebrew-bundle",
       HOMEBREW_LIBRARY/"Taps/homebrew/homebrew-foo",
diff --git a/Library/Homebrew/utils/lock.sh b/Library/Homebrew/utils/lock.sh
index ab6d2533db..cc041fa742 100644
--- a/Library/Homebrew/utils/lock.sh
+++ b/Library/Homebrew/utils/lock.sh
@@ -3,7 +3,7 @@
 # Noted due to the fixed FD, a shell process can only create one lock.
 lock() {
   local name="$1"
-  local lock_dir="$HOMEBREW_LIBRARY/Locks"
+  local lock_dir="$HOMEBREW_PREFIX/var/homebrew/locks"
   local lock_file="$lock_dir/$name"
   [[ -d "$lock_dir" ]] || mkdir -p "$lock_dir"
   # 200 is the file descriptor used in the lock.