diff --git a/tool/sync_default_gems.rb b/tool/sync_default_gems.rb
index cac3bec766..081ff63c39 100755
--- a/tool/sync_default_gems.rb
+++ b/tool/sync_default_gems.rb
@@ -436,8 +436,8 @@ module SyncDefaultGems
     |\.git.*
     |[A-Z]\w+file
     |COPYING
-    |\Arakelib\/.*
-    |\Atest\/lib\/.*
+    |rakelib\/.*
+    |test\/lib\/.*
     )\z/mx
 
   def message_filter(repo, sha, input: ARGF)
@@ -586,16 +586,32 @@ module SyncDefaultGems
         next
       end
 
-      tools = pipe_readlines(%W"git diff --name-only -z HEAD~..HEAD -- test/lib/ tool/ rakelib/")
+      changed = pipe_readlines(%W"git diff --name-only -z HEAD~..HEAD --")
+      toplevels = changed.map {|f| f[%r[\A(?!tool/)[^/]+/?]]}.compact
+      toplevels.delete_if do |top|
+        if system(*%w"git checkout -f HEAD~ --", top, err: File::NULL)
+          # previously existent path
+          system(*%w"git checkout -f HEAD --", top, out: File::NULL)
+          true
+        end
+      end
+      unless toplevels.empty?
+        puts "Remove files added to toplevel: #{toplevels.join(', ')}"
+        system(*%w"git rm -r --", *toplevels)
+      end
+      tools = changed.select {|f|f.start_with?("test/lib/", "tool/")}
       unless tools.empty?
-        system(*%W"git rm --", *tools)
+        system(*%W"git rm -r --", *tools)
         system(*%W"git checkout HEAD~ --", *tools)
+      end
+      unless toplevels.empty? and tools.empty?
+        clean = toplevels + tools
         if system(*%W"git diff --quiet HEAD~")
           `git reset HEAD~ --` && `git checkout .` && `git clean -fd`
-          puts "Skip commit #{sha} only for tools"
+          puts "Skip commit #{sha} only for tools or toplevel"
           next
         end
-        unless system(*%W"git commit --amend --no-edit --", *tools)
+        unless system(*%W"git commit --amend --no-edit --", *clean)
           failed_commits << sha
           `git reset HEAD~ --` && `git checkout .` && `git clean -fd`
           puts "Failed to pick #{sha}"
diff --git a/tool/test/test_sync_default_gems.rb b/tool/test/test_sync_default_gems.rb
index 39eab3f205..aa72dcfb20 100755
--- a/tool/test/test_sync_default_gems.rb
+++ b/tool/test/test_sync_default_gems.rb
@@ -93,6 +93,12 @@ module Test_SyncDefaultGems
       Dir.chdir(@testdir)
       ["src", @target].each do |dir|
         system(*%W"git init -q #{dir}", exception: true)
+        if dir == "src"
+          Dir.mkdir("#{dir}/lib")
+          File.write("#{dir}/lib/fine.rb", "return\n")
+          system(*%W"git add lib/fine.rb", exception: true, chdir: dir)
+          system(*%W"git commit -q -m", "Looks fine", exception: true, chdir: dir)
+        end
         Dir.mkdir("#{dir}/tool")
         File.write("#{dir}/tool/ok", "#!/bin/sh\n""echo ok\n")
         system(*%W"git add tool/ok", exception: true, chdir: dir)
@@ -147,5 +153,36 @@ module Test_SyncDefaultGems
       end
       assert_equal(@sha["src"], IO.popen(%W[git log --format=%H -1], chdir: "src", &:read).chomp, out)
     end
+
+    def test_skip_toplevel
+      Dir.mkdir("#@target/docs")
+      File.write("#@target/docs/NEWS.md", "= NEWS!!!\n")
+      system(*%W"git add --", "docs/NEWS.md", exception: true, chdir: @target)
+      system(*%W"git commit -q -m", "It's a news", exception: true, chdir: @target)
+      out = capture_process_output_to([STDOUT, STDERR]) do
+        Dir.chdir("src") do
+          SyncDefaultGems.sync_default_gems_with_commits(@target, true)
+        end
+      end
+      assert_equal(@sha["src"], IO.popen(%W[git log --format=%H -1], chdir: "src", &:read).chomp, out)
+    end
+
+    def test_adding_toplevel
+      Dir.mkdir("#@target/docs")
+      File.write("#@target/docs/NEWS.md", "= New library\n")
+      Dir.mkdir("#@target/lib")
+      File.write("#@target/lib/news.rb", "return\n")
+      system(*%W"git add --", "docs/NEWS.md", "lib/news.rb", exception: true, chdir: @target)
+      system(*%W"git commit -q -m", "New lib", exception: true, chdir: @target)
+      out = capture_process_output_to([STDOUT, STDERR]) do
+        Dir.chdir("src") do
+          SyncDefaultGems.sync_default_gems_with_commits(@target, true)
+        end
+      end
+      assert_not_equal(@sha["src"], IO.popen(%W[git log --format=%H -1], chdir: "src", &:read).chomp, out)
+      assert_equal "return\n", File.read("src/lib/news.rb")
+      assert_include IO.popen(%W[git log -1 --oneline], chdir: "src", &:read), "[ruby/#{@target}] New lib"
+      assert_not_operator File, :exist?, "src/docs"
+    end
   end
 end