diff --git a/cmd/entire/cli/strategy/content_overlap.go b/cmd/entire/cli/strategy/content_overlap.go
index f8d693887..83577ff5a 100644
--- a/cmd/entire/cli/strategy/content_overlap.go
+++ b/cmd/entire/cli/strategy/content_overlap.go
@@ -2,10 +2,13 @@ package strategy
 
 import (
 	"context"
+	"errors"
 	"io"
 	"log/slog"
 	"os"
+	"os/exec"
 	"path/filepath"
+	"time"
 
 	"github.com/entireio/cli/cmd/entire/cli/logging"
 	"github.com/go-git/go-git/v6"
@@ -493,7 +496,7 @@ func filesWithRemainingAgentChanges(
 		// Committed content differs from shadow. Check whether the working tree
 		// still has changes — if clean, the user intentionally replaced the content
 		// and there's nothing left to carry forward.
-		if worktreeRoot != "" && workingTreeMatchesCommit(worktreeRoot, filePath, commitFile.Hash) {
+		if worktreeRoot != "" && workingTreeMatchesCommit(ctx, worktreeRoot, filePath, commitFile.Hash) {
 			logging.Debug(logCtx, "filesWithRemainingAgentChanges: content differs from shadow but working tree is clean, skipping",
 				slog.String("file", filePath),
 				slog.String("commit_hash", commitFile.Hash.String()[:7]),
@@ -521,7 +524,22 @@ func filesWithRemainingAgentChanges(
 
 // workingTreeMatchesCommit checks if the file on disk matches the committed blob hash.
 // Returns true if the working tree is clean for this file (no remaining changes).
-func workingTreeMatchesCommit(worktreeRoot, filePath string, commitHash plumbing.Hash) bool {
+func workingTreeMatchesCommit(ctx context.Context, worktreeRoot, filePath string, commitHash plumbing.Hash) bool {
+	// Ask Git first so clean/smudge filters like core.autocrlf don't create
+	// phantom differences between the working tree bytes and the committed blob.
+	ctx, cancel := context.WithTimeout(ctx, 5*time.Second)
+	defer cancel()
+	cmd := exec.CommandContext(ctx, "git", "-C", worktreeRoot, "diff", "--exit-code", "--quiet", "--", filePath)
+	err := cmd.Run()
+	if err == nil {
+		return true
+	}
+	var exitErr *exec.ExitError
+	if errors.As(err, &exitErr) && exitErr.ExitCode() == 1 {
+		return false // git says file is dirty
+	}
+	// git itself failed (128+, timeout, etc.) — fall back to raw blob hash
+
 	absPath := filepath.Join(worktreeRoot, filePath)
 	diskContent, err := os.ReadFile(absPath) //nolint:gosec // filePath is from git status, not user input
 	if err != nil {
diff --git a/cmd/entire/cli/strategy/content_overlap_test.go b/cmd/entire/cli/strategy/content_overlap_test.go
index 65c149dd9..1bb6c6517 100644
--- a/cmd/entire/cli/strategy/content_overlap_test.go
+++ b/cmd/entire/cli/strategy/content_overlap_test.go
@@ -3,6 +3,7 @@ package strategy
 import (
 	"context"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"testing"
 	"time"
@@ -415,6 +416,58 @@ func TestFilesWithRemainingAgentChanges_ReplacedContent(t *testing.T) {
 	assert.Empty(t, remaining, "Replaced content with clean working tree should not be in remaining")
 }
 
+// TestFilesWithRemainingAgentChanges_AutocrlfNormalizedWorkingTree verifies that
+// line-ending normalization does not create phantom carry-forward files.
+func TestFilesWithRemainingAgentChanges_AutocrlfNormalizedWorkingTree(t *testing.T) {
+	t.Parallel()
+	dir := setupGitRepo(t)
+
+	repo, err := git.PlainOpen(dir)
+	require.NoError(t, err)
+
+	runGit := func(args ...string) {
+		t.Helper()
+		cmd := exec.CommandContext(context.Background(), "git", args...)
+		cmd.Dir = dir
+		out, err := cmd.CombinedOutput()
+		require.NoError(t, err, "git %v failed: %s", args, string(out))
+	}
+
+	runGit("config", "core.autocrlf", "true")
+
+	shadowContent := []byte("package main\r\n\r\nimport \"fmt\"\r\n\r\nfunc main() {\r\n\tfmt.Println(\"hello world\")\n\tfmt.Println(\"goodbye world\")\n}\n")
+	createShadowBranchWithContent(t, repo, "crlf123", "e3b0c4", map[string][]byte{
+		"src/main.go": shadowContent,
+	})
+
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "src"), 0o755))
+	workingTreeContent := []byte("package main\r\n\r\nimport \"fmt\"\r\n\r\nfunc main() {\r\n\tfmt.Println(\"hello world\")\r\n\tfmt.Println(\"goodbye world\")\r\n}\r\n")
+	testFile := filepath.Join(dir, "src", "main.go")
+	require.NoError(t, os.WriteFile(testFile, workingTreeContent, 0o644))
+
+	wt, err := repo.Worktree()
+	require.NoError(t, err)
+	_, err = wt.Add("src/main.go")
+	require.NoError(t, err)
+	headCommit, err := wt.Commit("Commit normalized content", &git.CommitOptions{
+		Author: &object.Signature{Name: "Test", Email: "test@test.com", When: time.Now()},
+	})
+	require.NoError(t, err)
+
+	commit, err := repo.CommitObject(headCommit)
+	require.NoError(t, err)
+
+	shadowBranch := checkpoint.ShadowBranchNameForCommit("crlf123", "e3b0c4")
+	committedFiles := map[string]struct{}{"src/main.go": {}}
+
+	// Git reports no diff here even though the on-disk bytes are CRLF and the
+	// committed blob is LF-normalized under core.autocrlf=true.
+	runGit("diff", "--exit-code", "--", "src/main.go")
+
+	remaining := filesWithRemainingAgentChanges(context.Background(), repo, shadowBranch, commit, []string{"src/main.go"}, committedFiles)
+	assert.Empty(t, remaining, "autocrlf-only working tree differences should not be carried forward")
+}
+
 // TestFilesWithRemainingAgentChanges_NoShadowBranch tests fallback to file-level subtraction.
 func TestFilesWithRemainingAgentChanges_NoShadowBranch(t *testing.T) {
 	t.Parallel()