diff --git a/tests/_lint/test_generated_with_comparison.py b/tests/_lint/test_generated_with_comparison.py
new file mode 100644
index 00000000000..fa6e729f1d7
--- /dev/null
+++ b/tests/_lint/test_generated_with_comparison.py
@@ -0,0 +1,123 @@
+# Copyright 2025 Marimo. All rights reserved.
+
+from marimo._lint.linter import _contents_differ_excluding_generated_with
+
+
+def test_contents_differ_excluding_generated_with():
+    """Test that __generated_with differences are ignored in content comparison."""
+
+    # Test case 1: Only __generated_with differs
+    original = """import marimo
+
+__generated_with = "0.8.0"
+app = marimo.App()
+
+@app.cell
+def test():
+    return
+
+if __name__ == "__main__":
+    app.run()
+"""
+
+    generated = """import marimo
+
+__generated_with = "0.9.0"
+app = marimo.App()
+
+@app.cell
+def test():
+    return
+
+if __name__ == "__main__":
+    app.run()
+"""
+
+    # Should return False (no meaningful differences)
+    assert not _contents_differ_excluding_generated_with(original, generated)
+
+
+def test_contents_differ_with_real_changes():
+    """Test that real code differences are detected."""
+
+    original = """import marimo
+
+__generated_with = "0.8.0"
+app = marimo.App()
+
+@app.cell
+def test():
+    x = 1
+    return
+
+if __name__ == "__main__":
+    app.run()
+"""
+
+    generated = """import marimo
+
+__generated_with = "0.9.0"
+app = marimo.App()
+
+@app.cell
+def test():
+    x = 2  # Changed value
+    return
+
+if __name__ == "__main__":
+    app.run()
+"""
+
+    # Should return True (real differences exist)
+    assert _contents_differ_excluding_generated_with(original, generated)
+
+
+def test_contents_no_generated_with():
+    """Test comparison when no __generated_with line exists."""
+
+    original = """import marimo
+
+app = marimo.App()
+
+@app.cell
+def test():
+    return
+"""
+
+    generated = """import marimo
+
+app = marimo.App()
+
+@app.cell
+def test():
+    return
+"""
+
+    # Should return False (identical content)
+    assert not _contents_differ_excluding_generated_with(original, generated)
+
+
+def test_contents_mixed_generated_with():
+    """Test when only one file has __generated_with."""
+
+    original = """import marimo
+
+app = marimo.App()
+
+@app.cell
+def test():
+    return
+"""
+
+    generated = """import marimo
+
+__generated_with = "0.9.0"
+app = marimo.App()
+
+@app.cell
+def test():
+    return
+"""
+
+    # Should return True (one has __generated_with, one doesn't)
+    assert _contents_differ_excluding_generated_with(original, generated)
diff --git a/tests/_lint/test_ignore_scripts.py b/tests/_lint/test_ignore_scripts.py
new file mode 100644
index 00000000000..4619694328e
--- /dev/null
+++ b/tests/_lint/test_ignore_scripts.py
@@ -0,0 +1,64 @@
+# Copyright 2025 Marimo. All rights reserved.
+
+from marimo._lint import run_check
+
+
+def test_ignore_scripts_flag(tmp_path):
+    """Test that --ignore-scripts suppresses errors for non-marimo files."""
+
+    # Create a temporary non-marimo Python file
+    temp_file = tmp_path / "test_script.py"
+    temp_file.write_text("""#!/usr/bin/env python3
+
+# This is a regular Python script, not a marimo notebook
+import os
+import sys
+
+def main():
+    print("Hello, world!")
+    return 0
+
+if __name__ == "__main__":
+    sys.exit(main())
+""")
+
+    # Test without ignore_scripts flag - should error
+    linter_with_error = run_check((str(temp_file),), ignore_scripts=False)
+    assert linter_with_error.errored is True
+    assert len(linter_with_error.files) == 1
+    assert linter_with_error.files[0].failed is True
+    assert "not a valid notebook" in linter_with_error.files[0].message
+
+    # Test with ignore_scripts flag - should not error
+    linter_ignore = run_check((str(temp_file),), ignore_scripts=True)
+    assert linter_ignore.errored is False
+    assert len(linter_ignore.files) == 1
+    assert linter_ignore.files[0].skipped is True
+    assert "not a marimo notebook" in linter_ignore.files[0].message
+
+
+def test_ignore_scripts_still_processes_marimo_files(tmp_path):
+    """Test that --ignore-scripts still processes valid marimo files."""
+
+    # Create a temporary marimo file
+    temp_file = tmp_path / "test_notebook.py"
+    temp_file.write_text("""import marimo
+
+__generated_with = "0.15.5"
+app = marimo.App()
+
+@app.cell
+def _():
+    import marimo as mo
+    return (mo,)
+
+if __name__ == "__main__":
+    app.run()
+""")
+
+    # Test with ignore_scripts flag - should still process marimo files
+    linter = run_check((str(temp_file),), ignore_scripts=True)
+    assert linter.errored is False
+    assert len(linter.files) == 1
+    assert linter.files[0].failed is False
+    assert linter.files[0].skipped is False