diff --git a/.gitignore b/.gitignore
index 03954e0..671845f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,3 +25,6 @@ usage_rules-*.tar
 
 # Temporary files, for example, from tests.
 /tmp/
+
+# Scratch test file
+test/scratch_test.exs
diff --git a/lib/mix/tasks/usage_rules.sync.ex b/lib/mix/tasks/usage_rules.sync.ex
index 4f1e312..34ccd29 100644
--- a/lib/mix/tasks/usage_rules.sync.ex
+++ b/lib/mix/tasks/usage_rules.sync.ex
@@ -853,7 +853,7 @@ if Code.ensure_loaded?(Igniter) do
                 acc,
                 ref_path,
                 content,
-                fn source -> Rewrite.Source.update(source, :content, content) end
+                fn source -> update_source_content(source, content) end
               )
           end
 
@@ -868,7 +868,7 @@ if Code.ensure_loaded?(Igniter) do
             inner_acc,
             ref_path,
             content,
-            fn source -> Rewrite.Source.update(source, :content, content) end
+            fn source -> update_source_content(source, content) end
           )
         end)
       end)
@@ -1038,7 +1038,7 @@ if Code.ensure_loaded?(Igniter) do
               acc2,
               dst_path,
               content,
-              fn source -> Rewrite.Source.update(source, :content, content) end
+              fn source -> update_source_content(source, content) end
             )
           end)
         end)
@@ -1346,20 +1346,50 @@ if Code.ensure_loaded?(Igniter) do
       if String.contains?(current_content, "<!-- usage-rules-skill-start -->") do
         custom = extract_skill_custom_content(current_content)
 
-        if custom != "" do
-          [new_frontmatter, new_managed] =
-            String.split(new_skill_md, "\n\n<!-- usage-rules-skill-start -->", parts: 2)
+        new_content =
+          if custom != "" do
+            [frontmatter, managed_body] =
+              String.split(new_skill_md, "\n\n<!-- usage-rules-skill-start -->", parts: 2)
 
-          new_frontmatter <>
-            "\n\n" <> custom <> "\n\n<!-- usage-rules-skill-start -->" <> new_managed
+            frontmatter <>
+              "\n\n" <> custom <> "\n\n<!-- usage-rules-skill-start -->" <> managed_body
+          else
+            new_skill_md
+          end
+
+        # Only return new content if the managed section actually changed.
+        # Rewrite.Source.write/2 applies eof_newline/1 which appends "\n"
+        # to disk content (see rewrite/lib/rewrite/source.ex, write/3 and
+        # eof_newline/1).  The generated content may not end with "\n", so
+        # subsequent reads see a trailing-whitespace diff that isn't a real
+        # change.  Comparing just the managed section avoids this.
+        if managed_section_changed?(current_content, new_content) do
+          new_content
         else
-          new_skill_md
+          current_content
         end
       else
         new_skill_md
       end
     end
 
+    defp managed_section_changed?(current, new) do
+      extract_managed_section(current) != extract_managed_section(new)
+    end
+
+    defp extract_managed_section(content) do
+      case String.split(content, "<!-- usage-rules-skill-start -->", parts: 2) do
+        [_, rest] ->
+          case String.split(rest, "<!-- usage-rules-skill-end -->", parts: 2) do
+            [managed, _] -> String.trim(managed)
+            _ -> String.trim(rest)
+          end
+
+        _ ->
+          nil
+      end
+    end
+
     defp strip_managed_skill_content(content) do
       # Remove managed-by metadata from frontmatter
       content = String.replace(content, ~r/metadata:\n\s+managed-by: usage-rules\n/, "")
@@ -1385,6 +1415,21 @@ if Code.ensure_loaded?(Igniter) do
       String.replace(content, ~r/\A\s*<!--\s*\n(?:.*?SPDX-.*?\n)*.*?-->\s*\n*/s, "")
     end
 
+    # Updates a reference file's content, ignoring trailing whitespace differences.
+    # Reference files have no managed-section markers — the entire file is synced
+    # content.  Rewrite.Source.write/2 applies eof_newline/1 (see
+    # rewrite/lib/rewrite/source.ex) which appends "\n" when writing to disk,
+    # but dep content may not end with one, causing false diffs on subsequent syncs.
+    defp update_source_content(source, new_content) do
+      current = Rewrite.Source.get(source, :content)
+
+      if String.trim_trailing(current) == String.trim_trailing(new_content) do
+        source
+      else
+        Rewrite.Source.update(source, :content, new_content)
+      end
+    end
+
     defp format_yaml_string(str) do
       str = String.trim(str)
 
diff --git a/test/mix/tasks/usage_rules.sync_test.exs b/test/mix/tasks/usage_rules.sync_test.exs
index d670dcf..bf66cb8 100644
--- a/test/mix/tasks/usage_rules.sync_test.exs
+++ b/test/mix/tasks/usage_rules.sync_test.exs
@@ -1455,4 +1455,189 @@ defmodule Mix.Tasks.UsageRules.SyncTest do
       |> assert_creates(".claude/skills/foo-built/SKILL.md")
     end
   end
+
+  describe "idempotency (--check)" do
+    # Rewrite.Source.write/2 calls eof_newline/1 before File.write/2
+    # (see rewrite/lib/rewrite/source.ex line ~297 and ~970):
+    #
+    #   defp write(%Source{path: path, content: content}, ...) do
+    #     file_write(path, eof_newline(content))
+    #   end
+    #   defp eof_newline(string), do: String.trim_trailing(string) <> "\n"
+    #
+    # In test mode, simulate_write stores raw content without this
+    # normalization, so tests don't reproduce the trailing-newline mismatch
+    # that causes --check failures in real usage.  This helper applies the
+    # same eof_newline transform to simulate a real disk round-trip.
+    defp simulate_disk_roundtrip(igniter) do
+      test_files =
+        Enum.reduce(igniter.assigns[:test_files], igniter.assigns[:test_files], fn
+          {"deps/" <> _, _content}, acc ->
+            acc
+
+          {_path, ""}, acc ->
+            acc
+
+          {path, content}, acc ->
+            Map.put(acc, path, String.trim_trailing(content) <> "\n")
+        end)
+
+      igniter
+      |> Map.put(:rewrite, Rewrite.new())
+      |> Map.put(:assigns, %{
+        test_mode?: true,
+        test_files: test_files,
+        igniter_exs: igniter.assigns[:igniter_exs]
+      })
+      |> Igniter.include_glob("**/*.*")
+    end
+
+    test "second sync reports no changes for skills.build" do
+      config = [
+        skills: [
+          location: ".claude/skills",
+          build: [
+            "use-foo": [
+              description: "Foo skill",
+              usage_rules: [:foo, :bar]
+            ]
+          ]
+        ]
+      ]
+
+      igniter =
+        project_with_deps(%{
+          "deps/foo/usage-rules.md" => "# Foo Rules\n\nUse foo wisely.",
+          "deps/bar/usage-rules.md" => "# Bar Rules\n\nUse bar wisely."
+        })
+        |> sync(config)
+        |> assert_creates(".claude/skills/use-foo/SKILL.md")
+        |> assert_creates(".claude/skills/use-foo/references/foo.md")
+        |> assert_creates(".claude/skills/use-foo/references/bar.md")
+        |> apply_igniter!()
+        |> simulate_disk_roundtrip()
+
+      igniter
+      |> sync(config)
+      |> assert_unchanged()
+    end
+
+    test "second sync reports no changes for skills.deps" do
+      config = [
+        skills: [
+          location: ".claude/skills",
+          deps: [:foo]
+        ]
+      ]
+
+      igniter =
+        project_with_deps(%{
+          "deps/foo/usage-rules.md" => "# Foo Rules\n\nUse foo wisely."
+        })
+        |> sync(config)
+        |> assert_creates(".claude/skills/use-foo/SKILL.md")
+        |> apply_igniter!()
+        |> simulate_disk_roundtrip()
+
+      igniter
+      |> sync(config)
+      |> assert_unchanged()
+    end
+
+    test "second sync reports no changes for AGENTS.md" do
+      config = [
+        file: "AGENTS.md",
+        usage_rules: [:foo]
+      ]
+
+      igniter =
+        project_with_deps(%{
+          "deps/foo/usage-rules.md" => "# Foo Rules\n\nUse foo wisely."
+        })
+        |> sync(config)
+        |> assert_creates("AGENTS.md")
+        |> apply_igniter!()
+        |> simulate_disk_roundtrip()
+
+      igniter
+      |> sync(config)
+      |> assert_unchanged()
+    end
+
+    test "second sync reports no changes with sub-rules" do
+      config = [
+        skills: [
+          location: ".claude/skills",
+          build: [
+            "use-foo": [usage_rules: [:foo]]
+          ]
+        ]
+      ]
+
+      igniter =
+        project_with_deps(%{
+          "deps/foo/usage-rules.md" => "# Foo Rules",
+          "deps/foo/usage-rules/testing.md" => "# Testing Guide"
+        })
+        |> sync(config)
+        |> assert_creates(".claude/skills/use-foo/SKILL.md")
+        |> assert_creates(".claude/skills/use-foo/references/foo.md")
+        |> assert_creates(".claude/skills/use-foo/references/testing.md")
+        |> apply_igniter!()
+        |> simulate_disk_roundtrip()
+
+      igniter
+      |> sync(config)
+      |> assert_unchanged()
+    end
+
+    test "second sync reports no changes with custom content in SKILL.md" do
+      config = [
+        skills: [
+          location: ".claude/skills",
+          build: [
+            "use-foo": [
+              description: "Foo skill",
+              usage_rules: [:foo]
+            ]
+          ]
+        ]
+      ]
+
+      # First sync creates the skill
+      igniter =
+        project_with_deps(%{
+          "deps/foo/usage-rules.md" => "# Foo Rules\n\nUse foo wisely."
+        })
+        |> sync(config)
+        |> assert_creates(".claude/skills/use-foo/SKILL.md")
+        |> assert_creates(".claude/skills/use-foo/references/foo.md")
+        |> apply_igniter!()
+
+      # Inject custom content between frontmatter and managed section
+      skill_content = igniter.assigns[:test_files][".claude/skills/use-foo/SKILL.md"]
+
+      [frontmatter, managed] =
+        String.split(skill_content, "\n\n<!-- usage-rules-skill-start -->", parts: 2)
+
+      custom_skill =
+        frontmatter <>
+          "\n\nMy custom instructions go here.\n\n<!-- usage-rules-skill-start -->" <>
+          managed
+
+      test_files =
+        Map.put(igniter.assigns[:test_files], ".claude/skills/use-foo/SKILL.md", custom_skill)
+
+      igniter = put_in(igniter.assigns[:test_files], test_files)
+
+      igniter =
+        igniter
+        |> simulate_disk_roundtrip()
+
+      # Second sync should preserve custom content and report no changes
+      igniter
+      |> sync(config)
+      |> assert_unchanged()
+    end
+  end
 end