fix(setup): preserve selected home paths throughout skill installation

tests/acceptance/setup/selectedClientHomePaths.test.ts

@@ -109,3 +109,96 @@ cliTest.skipIf(process.platform === "win32")(
     ).toEqual([]);
   },
 );
+
+cliTest.skipIf(process.platform === "win32")(
+  "installs shared skills in the native HOME selection with backups and repeat setup",
+  async ({ cli }) => {
+    const root = await createTestTempDirectory("rea-selected-skill-home-");
+    const selected = join(root, "selected");
+    await mkdir(join(selected, "nested"), { recursive: true });
+    await symlink(join(selected, "nested"), join(root, "alias"));
+    const home = `${root}/alias/..`;
+    const relative = ".agents/skills/reverse-engineer-anything";
+    const skill = join(selected, relative);
+    const lexicalSkill = join(root, relative);
+    const original = "previous selected instructions\n";
+    const oldReference = "previous selected reference\n";
+    const sentinel = "unselected instructions\n";
+    const sentinelReference = "unselected reference\n";
+    const reference = "references/connection-and-recovery.md";
+    for (const directory of [skill, lexicalSkill])
+      await mkdir(join(directory, "references"), { recursive: true });
+    await writeFile(join(skill, "SKILL.md"), original);
+    await writeFile(join(skill, reference), oldReference);
+    await writeFile(join(lexicalSkill, "SKILL.md"), sentinel);
+    await writeFile(join(lexicalSkill, reference), sentinelReference);
+    const run = (arguments_: readonly string[]) =>
+      cli.run({
+        arguments: [...arguments_, "--json"],
+        cwd: root,
+        environment: { HOME: home, USERPROFILE: home },
+      });
+    const configured = await run([
+      "setup",
+      "--skill-client",
+      "shared",
+      "--yes",
+    ]);
+    expect(configured.exitCode, configured.stdout + configured.stderr).toBe(0);
+    expect(configured.json).toMatchObject({
+      status: "ready",
+      appliedActions: ["installed_skill"],
+    });
+    const installed = await readFile(join(skill, "SKILL.md"), "utf8");
+    expect(installed).toContain("name: reverse-engineer-anything");
+    const installedReference = await readFile(join(skill, reference), "utf8");
+    expect(installedReference).not.toBe(oldReference);
+    expect(await readFile(join(skill, "SKILL.md.rea.backup"), "utf8")).toBe(
+      original,
+    );
+    expect(await readFile(`${join(skill, reference)}.rea.backup`, "utf8")).toBe(
+      oldReference,
+    );
+    expect(await readFile(join(lexicalSkill, "SKILL.md"), "utf8")).toBe(
+      sentinel,
+    );
+    expect(await readFile(join(lexicalSkill, reference), "utf8")).toBe(
+      sentinelReference,
+    );
+    for (const path of [
+      join(lexicalSkill, "SKILL.md.rea.backup"),
+      `${join(lexicalSkill, reference)}.rea.backup`,
+    ])
+      await expect(access(path)).rejects.toMatchObject({ code: "ENOENT" });
+    const repeated = await run(["setup", "--skill-client", "shared", "--yes"]);
+    expect(repeated.exitCode, repeated.stdout + repeated.stderr).toBe(0);
+    expect(repeated.json).toMatchObject({
+      status: "ready",
+      appliedActions: [],
+    });
+    expect(await readFile(join(skill, "SKILL.md"), "utf8")).toBe(installed);
+    expect(await readFile(join(skill, reference), "utf8")).toBe(
+      installedReference,
+    );
+    const doctor = await run(["doctor", "--skill"]);
+    // Doctor also discovers client-specific locations. Gemini uses the lexical
+    // HOME sibling, whose deliberately stale sentinel must remain untouched.
+    expect(doctor.exitCode, doctor.stdout + doctor.stderr).toBe(1);
+    expect(doctor.json).toMatchObject({
+      identity: {
+        skill: {
+          state: "stale",
+          issues: [{ client: "gemini_cli", path: lexicalSkill, kind: "stale" }],
+        },
+      },
+    });
+    expect(
+      (await readdir(skill)).filter((name) => name.startsWith(".rea-skill-")),
+    ).toEqual([]);
+    expect(
+      (await readdir(join(skill, "references"))).filter((name) =>
+        name.startsWith(".rea-skill-"),
+      ),
+    ).toEqual([]);
+  },
+);