Print warning if deprecated --include-python flag is given

test/e2e/include-python-deprecation.e2e.spec.js

@@ -0,0 +1,45 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: deprecated --include-python handling", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  for (let shell of ["bash", "zsh"]) {
+    it(`safe-chain setup warns and continues for ${shell}`, async () => {
+      const sh = await container.openShell(shell);
+      const result = await sh.runCommand("safe-chain setup --include-python");
+
+      assert.ok(
+        result.output.toLowerCase().includes("deprecated and ignored"),
+        `Expected warning about deprecated --include-python. Output was:\n${result.output}`
+      );
+    });
+
+    it(`safe-chain setup-ci warns and continues for ${shell}`, async () => {
+      const sh = await container.openShell(shell);
+      const result = await sh.runCommand("safe-chain setup-ci --include-python");
+
+      assert.ok(
+        result.output.toLowerCase().includes("deprecated and ignored"),
+        `Expected warning about deprecated --include-python. Output was:\n${result.output}`
+      );
+    });
+  }
+});