diff --git a/Library/Homebrew/caveats.rb b/Library/Homebrew/caveats.rb
index 350e2d57b3..7c23901b85 100644
--- a/Library/Homebrew/caveats.rb
+++ b/Library/Homebrew/caveats.rb
@@ -169,7 +169,7 @@ class Caveats
       # we readlink because this path probably doesn't exist since caveats
       # occurs before the link step of installation
       # Yosemite security measures mildly tighter rules:
-      # https://github.com/Homebrew/homebrew/issues/33815
+      # https://github.com/Homebrew/legacy-homebrew/issues/33815
       if !plist_path.file? || !plist_path.symlink?
         if f.plist_startup
           s << "To have launchd start #{f.full_name} now and restart at startup:"
diff --git a/Library/Homebrew/cmd/pull.rb b/Library/Homebrew/cmd/pull.rb
index 33868d8f77..93470dc481 100644
--- a/Library/Homebrew/cmd/pull.rb
+++ b/Library/Homebrew/cmd/pull.rb
@@ -18,7 +18,7 @@
 #   --resolve:   When a patch fails to apply, leave in progress and allow user to
 #                 resolve, instead of aborting
 #   --branch-okay: Do not warn if pulling to a branch besides master (useful for testing)
-#   --legacy:    Pull legacy formula PR from Homebrew/homebrew
+#   --legacy:    Pull legacy formula PR from Homebrew/legacy-homebrew
 #                (TODO remove it when it's not longer necessary)
 
 require "utils"
diff --git a/Library/Homebrew/cmd/test-bot.rb b/Library/Homebrew/cmd/test-bot.rb
index 3ac338b6d3..6ffba45c23 100644
--- a/Library/Homebrew/cmd/test-bot.rb
+++ b/Library/Homebrew/cmd/test-bot.rb
@@ -11,7 +11,7 @@
 # --junit:         Generate a JUnit XML test results file.
 # --no-bottle:     Run brew install without --build-bottle.
 # --keep-old:      Run brew bottle --keep-old to build new bottles for a single platform.
-# --legacy         Build formula from legacy Homebrew/homebrew repo.
+# --legacy         Build formula from legacy Homebrew/legacy-homebrew repo.
 #                  (TODO remove it when it's not longer necessary)
 # --HEAD:          Run brew install with --HEAD.
 # --local:         Ask Homebrew to write verbose logs under ./logs/ and set HOME to ./home/.
@@ -336,7 +336,7 @@ module Homebrew
         @name = @hash
       # Handle a URL being passed on the command-line or through Jenkins/Travis
       # environment variables e.g.
-      # `brew test-bot https://github.com/Homebrew/homebrew/pull/44293`.
+      # `brew test-bot https://github.com/Homebrew/homebrew-core/pull/678`.
       elsif @url
         # TODO: in future Travis CI may need to also use `brew pull` to e.g. push
         # the right commit to BrewTestBot.
diff --git a/Library/Homebrew/diagnostic.rb b/Library/Homebrew/diagnostic.rb
index a048f07619..d79e540c14 100644
--- a/Library/Homebrew/diagnostic.rb
+++ b/Library/Homebrew/diagnostic.rb
@@ -85,7 +85,7 @@ module Homebrew
       end
       ############# END HELPERS
 
-      # See https://github.com/Homebrew/homebrew/pull/9986
+      # See https://github.com/Homebrew/legacy-homebrew/pull/9986
       def check_path_for_trailing_slashes
         all_paths = ENV["PATH"].split(File::PATH_SEPARATOR)
         bad_paths = all_paths.select { |p| p[-1..-1] == "/" }
diff --git a/Library/Homebrew/formula.rb b/Library/Homebrew/formula.rb
index a6bc2cbe0b..f1ca9ec23f 100644
--- a/Library/Homebrew/formula.rb
+++ b/Library/Homebrew/formula.rb
@@ -25,7 +25,7 @@ require "migrator"
 # @see SharedEnvExtension
 # @see FileUtils
 # @see Pathname
-# @see http://www.rubydoc.info/github/Homebrew/homebrew/file/share/doc/homebrew/Formula-Cookbook.md Formula Cookbook
+# @see http://www.rubydoc.info/github/Homebrew/brew/file/share/doc/homebrew/Formula-Cookbook.md Formula Cookbook
 # @see https://github.com/styleguide/ruby Ruby Style Guide
 #
 # <pre>class Wget < Formula
diff --git a/Library/Homebrew/language/haskell.rb b/Library/Homebrew/language/haskell.rb
index b2aa1c5054..947683ccdc 100644
--- a/Library/Homebrew/language/haskell.rb
+++ b/Library/Homebrew/language/haskell.rb
@@ -46,7 +46,7 @@ module Language
 
       def cabal_install(*args)
         # cabal hardcodes 64 as the maximum number of parallel jobs
-        # https://github.com/Homebrew/homebrew/issues/49509
+        # https://github.com/Homebrew/legacy-homebrew/issues/49509
         make_jobs = ENV.make_jobs > 64 ? 64 : ENV.make_jobs
 
         # cabal-install's dependency-resolution backtracking strategy can easily
diff --git a/Library/Homebrew/os/mac.rb b/Library/Homebrew/os/mac.rb
index d2e115acf5..54568befd8 100644
--- a/Library/Homebrew/os/mac.rb
+++ b/Library/Homebrew/os/mac.rb
@@ -97,7 +97,7 @@ module OS
     #      named after a newer OS version than the running OS. The
     #      MACOSX_DEPLOYMENT_TARGET must be set to the OS for which you're
     #      actually building (usually the running OS version).
-    #      https://github.com/Homebrew/homebrew/pull/50355
+    #      https://github.com/Homebrew/legacy-homebrew/pull/50355
     #      https://developer.apple.com/library/ios/documentation/DeveloperTools/Conceptual/WhatsNewXcode/Articles/Introduction.html#//apple_ref/doc/uid/TP40004626
     #      Section "About SDKs and Simulator"
     #   b) For Xcode < 7, proceed as if the SDK for the running OS version had
@@ -205,9 +205,9 @@ module OS
     end
 
     # See these issues for some history:
-    # https://github.com/Homebrew/homebrew/issues/13
-    # https://github.com/Homebrew/homebrew/issues/41
-    # https://github.com/Homebrew/homebrew/issues/48
+    # https://github.com/Homebrew/legacy-homebrew/issues/13
+    # https://github.com/Homebrew/legacy-homebrew/issues/41
+    # https://github.com/Homebrew/legacy-homebrew/issues/48
     def macports_or_fink
       paths = []
 
diff --git a/Library/Homebrew/test/Gemfile b/Library/Homebrew/test/Gemfile
index fb783b9b2f..5fb41787df 100644
--- a/Library/Homebrew/test/Gemfile
+++ b/Library/Homebrew/test/Gemfile
@@ -6,7 +6,7 @@ gem "rake", "~> 10.3"
 # This is a patched version of the v0.11.2. Switch back to the stable version
 # when #436 has been merged upstream.
 # https://github.com/colszowka/simplecov/pull/436
-# See also https://github.com/Homebrew/homebrew/pull/48250#issuecomment-173171990
+# See also https://github.com/Homebrew/legacy-homebrew/pull/48250#issuecomment-173171990
 gem "simplecov", "0.11.2",
   :git => "https://github.com/Homebrew/simplecov.git",
   :branch => "tracked-files-root-fix",
diff --git a/Library/Homebrew/test/test_cmd_audit.rb b/Library/Homebrew/test/test_cmd_audit.rb
index 0a441764f9..b5ec51bfee 100644
--- a/Library/Homebrew/test/test_cmd_audit.rb
+++ b/Library/Homebrew/test/test_cmd_audit.rb
@@ -318,7 +318,7 @@ class FormulaAuditorTests < Homebrew::TestCase
     assert_equal [], fa.problems
   end
 
-  # Regression test for https://github.com/Homebrew/homebrew/pull/48744
+  # Regression test for https://github.com/Homebrew/legacy-homebrew/pull/48744
   # Formulae with "++" in their name would break various audit regexps:
   #   Error: nested *?+ in regexp: /^libxml++3\s/
   def test_audit_plus_plus_name
diff --git a/Library/Homebrew/test/test_integration_cmds.rb b/Library/Homebrew/test/test_integration_cmds.rb
index 63076a4df6..865daa5203 100644
--- a/Library/Homebrew/test/test_integration_cmds.rb
+++ b/Library/Homebrew/test/test_integration_cmds.rb
@@ -170,7 +170,7 @@ class IntegrationCommandTests < Homebrew::TestCase
       end
     EOS
     # `brew bottle` should not fail with dead symlink
-    # https://github.com/Homebrew/homebrew/issues/49007
+    # https://github.com/Homebrew/legacy-homebrew/issues/49007
     (HOMEBREW_CELLAR/"testball/0.1").cd do
       FileUtils.ln_s "not-exist", "symlink"
     end
diff --git a/Library/Homebrew/test/test_utils.rb b/Library/Homebrew/test/test_utils.rb
index 128b26dea0..08e95e190c 100644
--- a/Library/Homebrew/test/test_utils.rb
+++ b/Library/Homebrew/test/test_utils.rb
@@ -103,7 +103,7 @@ class UtilTests < Homebrew::TestCase
 
   def test_which_skip_malformed_path
     # 'which' should not fail if a path is malformed
-    # see https://github.com/Homebrew/homebrew/issues/32789 for an example
+    # see https://github.com/Homebrew/legacy-homebrew/issues/32789 for an example
     cmd = @dir/"foo"
     FileUtils.touch cmd
     cmd.chmod 0744
diff --git a/Library/Homebrew/utils.rb b/Library/Homebrew/utils.rb
index d1d7b540ee..c2b0dd231a 100644
--- a/Library/Homebrew/utils.rb
+++ b/Library/Homebrew/utils.rb
@@ -399,7 +399,7 @@ def which(cmd, path = ENV["PATH"])
       pcmd = File.expand_path(cmd, p)
     rescue ArgumentError
       # File.expand_path will raise an ArgumentError if the path is malformed.
-      # See https://github.com/Homebrew/homebrew/issues/32789
+      # See https://github.com/Homebrew/legacy-homebrew/issues/32789
       next
     end
     return Pathname.new(pcmd) if File.file?(pcmd) && File.executable?(pcmd)
@@ -413,7 +413,7 @@ def which_all(cmd, path = ENV["PATH"])
       pcmd = File.expand_path(cmd, p)
     rescue ArgumentError
       # File.expand_path will raise an ArgumentError if the path is malformed.
-      # See https://github.com/Homebrew/homebrew/issues/32789
+      # See https://github.com/Homebrew/legacy-homebrew/issues/32789
       next
     end
     Pathname.new(pcmd) if File.file?(pcmd) && File.executable?(pcmd)