diff --git a/src/application/SupportedClients.ts b/src/application/SupportedClients.ts
index 460126c34e..198f909afd 100644
--- a/src/application/SupportedClients.ts
+++ b/src/application/SupportedClients.ts
@@ -7,6 +7,7 @@ import {
   resolveHermesClientHome,
 } from "./HermesClientHome.js";
 import { compareUnicodeCodePoints } from "../domain/unicodeCodePointOrder.js";
+import { appendCallerPath } from "../filesystem/callerPath.js";
 import { resolveWindowsClaudeDesktopLocation } from "./ClaudeDesktopConfigLocation.js";
 import {
   type MsixPackageView,
@@ -524,7 +525,7 @@ export const SUPPORTED_CLIENT_DEFINITIONS = [
     name: "codex",
     displayName: "Codex",
     configPath: (context: ClientPathContext) =>
-      join(codexDirectory(context), "config.toml"),
+      appendCallerPath(codexDirectory(context), "config.toml"),
     markerPath: codexDirectory,
     format: "toml",
   },
diff --git a/tests/acceptance/setup/selectedClientHomePaths.test.ts b/tests/acceptance/setup/selectedClientHomePaths.test.ts
new file mode 100644
index 0000000000..dc69c88a72
--- /dev/null
+++ b/tests/acceptance/setup/selectedClientHomePaths.test.ts
@@ -0,0 +1,111 @@
+import {
+  access,
+  mkdir,
+  readFile,
+  readdir,
+  symlink,
+  writeFile,
+} from "node:fs/promises";
+import { dirname, join } from "node:path";
+
+import { expect } from "vitest";
+
+import { parseClientConfiguration } from "../../../src/application/ClientConfigurationDocument.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { cliTest } from "../../support/cli/cliFixture.js";
+
+cliTest.skipIf(process.platform === "win32")(
+  "configures Codex in the filesystem-selected CODEX_HOME and shared skills in HOME with backups and repeat setup",
+  async ({ cli }) => {
+    const root = await createTestTempDirectory("rea-selected-client-home-");
+    const selected = join(root, "selected");
+    await mkdir(join(selected, "deep"), { recursive: true });
+    await symlink(join(selected, "deep"), join(root, "link"));
+    const home = join(root, "home");
+    await mkdir(home);
+    const codexHome = `${root}/link/..`;
+    const config = join(selected, "config.toml");
+    const lexicalConfig = join(root, "config.toml");
+    const original =
+      'model = "selected-model"\n[mcp_servers.other]\ncommand = "other-server"\n';
+    const sentinel = 'model = "unselected-model"\n';
+    await mkdir(dirname(config), { recursive: true });
+    await mkdir(dirname(lexicalConfig), { recursive: true });
+    await writeFile(config, original);
+    await writeFile(lexicalConfig, sentinel);
+    const manifest = join(
+      home,
+      ".agents/skills/reverse-engineer-anything/SKILL.md",
+    );
+    const lexicalManifest = join(
+      root,
+      ".agents/skills/reverse-engineer-anything/SKILL.md",
+    );
+    await mkdir(dirname(manifest), { recursive: true });
+    await mkdir(dirname(lexicalManifest), { recursive: true });
+    const originalSkill = "previous selected instructions\n";
+    const sentinelSkill = "unselected instructions\n";
+    await writeFile(manifest, originalSkill);
+    await writeFile(lexicalManifest, sentinelSkill);
+    const run = () =>
+      cli.run({
+        arguments: [
+          "setup",
+          "--client",
+          "codex",
+          "--skill-client",
+          "codex",
+          "--yes",
+          "--json",
+        ],
+        cwd: root,
+        environment: {
+          HOME: home,
+          USERPROFILE: home,
+          CODEX_HOME: codexHome,
+          HOPPER_LAUNCHER_PATH: join(root, "missing-hopper"),
+          GHIDRA_INSTALL_DIR: join(root, "missing-ghidra"),
+          JAVA_HOME: join(root, "missing-java"),
+        },
+      });
+    const configured = await run();
+    expect(configured.exitCode, configured.stdout + configured.stderr).toBe(0);
+    const registered = parseClientConfiguration(
+      await readFile(config, "utf8"),
+      "toml",
+    );
+    expect(registered.document.model).toBe("selected-model");
+    expect(registered.servers.other).toMatchObject({ command: "other-server" });
+    expect(registered.servers.rea).toBeDefined();
+    const installed = await readFile(manifest, "utf8");
+    expect(installed).toContain("name: reverse-engineer-anything");
+    expect(await readFile(`${config}.rea.backup`, "utf8")).toBe(original);
+    expect(await readFile(`${manifest}.rea.backup`, "utf8")).toBe(
+      originalSkill,
+    );
+    expect(await readFile(lexicalConfig, "utf8")).toBe(sentinel);
+    expect(await readFile(lexicalManifest, "utf8")).toBe(sentinelSkill);
+    await expect(access(`${lexicalConfig}.rea.backup`)).rejects.toMatchObject({
+      code: "ENOENT",
+    });
+    await expect(access(`${lexicalManifest}.rea.backup`)).rejects.toMatchObject(
+      { code: "ENOENT" },
+    );
+    const before = await readFile(config);
+    const repeated = await run();
+    expect(repeated.exitCode, repeated.stdout + repeated.stderr).toBe(0);
+    expect(repeated.json).toMatchObject({
+      status: "ready",
+      appliedActions: [],
+    });
+    expect((await readFile(config)).equals(before)).toBe(true);
+    expect(await readFile(manifest, "utf8")).toBe(installed);
+    expect(await readFile(lexicalConfig, "utf8")).toBe(sentinel);
+    expect(await readFile(lexicalManifest, "utf8")).toBe(sentinelSkill);
+    expect(
+      (await readdir(dirname(manifest))).filter((name) =>
+        name.startsWith(".rea-skill-"),
+      ),
+    ).toEqual([]);
+  },
+);