diff --git a/src/application/ClientRegistration.ts b/src/application/ClientRegistration.ts
index 0d9e4d6841..ec38c6d7c1 100644
--- a/src/application/ClientRegistration.ts
+++ b/src/application/ClientRegistration.ts
@@ -21,22 +21,36 @@ const tomlTimeoutSchema = z.union([
   z.bigint().positive(),
 ]);
 
-/** Common launcher facts, without assigning a shared meaning to client policy. */
-const registrationSchema = z
+const launcherSchema = z
   .object({
     command: z.string().min(1),
     args: z.array(z.string()).default([]),
-    startup_timeout_sec: tomlTimeoutSchema.optional(),
-    tool_timeout_sec: tomlTimeoutSchema.optional(),
-    startupTimeoutMs: z.number().positive().optional(),
-    toolTimeoutMs: z.number().positive().optional(),
-    type: z.string().optional(),
-    transport: z.string().optional(),
-    serverName: z.string().optional(),
-    disabled: z.boolean().optional(),
-    enabled: z.boolean().optional(),
   })
   .passthrough();
+const opencodeLauncherSchema = z
+  .object({
+    type: z.literal("local"),
+    command: z.array(z.string()).min(1),
+  })
+  .passthrough();
+const normalizeOpencodeLauncher = (
+  entry: z.output<typeof opencodeLauncherSchema>,
+): z.output<typeof launcherSchema> => {
+  const [command = "", ...args] = entry.command;
+  return { ...entry, command, args };
+};
+
+const registrationSchema = launcherSchema.extend({
+  startup_timeout_sec: tomlTimeoutSchema.optional(),
+  tool_timeout_sec: tomlTimeoutSchema.optional(),
+  startupTimeoutMs: z.number().positive().optional(),
+  toolTimeoutMs: z.number().positive().optional(),
+  type: z.string().optional(),
+  transport: z.string().optional(),
+  serverName: z.string().optional(),
+  disabled: z.boolean().optional(),
+  enabled: z.boolean().optional(),
+});
 
 export type ClientRegistration = z.output<typeof registrationSchema>;
 
@@ -76,6 +90,22 @@ const registrationError = (error: z.ZodError): ConfigurationError =>
     })),
   });
 
+/** Launcher identity remains usable when unrelated readiness settings are invalid. */
+export const parseClientRegistrationLauncher = (
+  value: unknown,
+  client: SetupClient,
+): Result<{ command: string; args: string[] }, ConfigurationError> => {
+  const parsed =
+    client.format === "opencode"
+      ? opencodeLauncherSchema
+          .transform(normalizeOpencodeLauncher)
+          .safeParse(value)
+      : launcherSchema.safeParse(value);
+  return parsed.success
+    ? ok({ command: parsed.data.command, args: parsed.data.args })
+    : err(registrationError(parsed.error));
+};
+
 /** Policy belongs to the client dialect, and is validated before refresh writes. */
 const validateClientPolicy = (
   value: unknown,
@@ -109,17 +139,14 @@ export const parseClientRegistration = (
       : err(registrationError(parsed.error));
   }
   if (client.format === "opencode") {
-    const entry = z
-      .object({
-        type: z.literal("local"),
-        command: z.array(z.string()).min(1),
+    const entry = opencodeLauncherSchema
+      .extend({
         environment: z.record(z.string(), z.string()).optional(),
       })
-      .passthrough()
+      .transform(normalizeOpencodeLauncher)
       .safeParse(value);
     if (!entry.success) return err(registrationError(entry.error));
-    const [command = "", ...args] = entry.data.command;
-    value = { ...entry.data, command, args };
+    value = entry.data;
   }
   const parsed = registrationSchema.safeParse(value);
   if (!parsed.success) return err(registrationError(parsed.error));
@@ -182,7 +209,7 @@ export const refreshClientRegistration = (
   const existing = source.success ? source.data : {};
   const policy = validateClientPolicy(existing, client);
   if (!policy.ok) return policy;
-  const prior = parseClientRegistration(existing, client);
+  const prior = parseClientRegistrationLauncher(existing, client);
   const priorCommand = prior.ok
     ? [prior.value.command, ...prior.value.args]
     : undefined;
diff --git a/src/application/Uninstall.ts b/src/application/Uninstall.ts
index a950313657..9db087b5d7 100644
--- a/src/application/Uninstall.ts
+++ b/src/application/Uninstall.ts
@@ -22,7 +22,7 @@ import { defaultKunaCacheDirectory } from "../config/kunaCacheDirectory.js";
 import { linuxHopperReleaseCacheDirectory } from "./LinuxHopperCacheDirectory.js";
 
 import { ClientConfigurationPublication } from "./ClientConfigurationPublication.js";
-import { z } from "zod";
+import { parseClientRegistrationLauncher } from "./ClientRegistration.js";
 
 import { PRODUCT_IDENTITY } from "../identity.js";
 import {
@@ -734,21 +734,9 @@ const resolveUninstallConfigPath = async (
 
 /** Ownership rule for persistent MCP registrations created by REA setup. */
 const isOwnedRegistration = (value: unknown, client: SetupClient): boolean => {
-  if (client.format === "opencode") {
-    const parsed = z
-      .object({ type: z.literal("local"), command: z.array(z.string()).min(1) })
-      .passthrough()
-      .safeParse(value);
-    if (!parsed.success) return false;
-    const command = parsed.data.command;
-    return (
-      classifyClientRegistrationCommand(command, CURRENT_ENTRYPOINT_PATH) ===
-      "owned"
-    );
-  }
-  const parsed = registrationSchema.safeParse(value);
-  if (!parsed.success) return false;
-  const { command, args } = parsed.data;
+  const parsed = parseClientRegistrationLauncher(value, client);
+  if (!parsed.ok) return false;
+  const { command, args } = parsed.value;
   return (
     classifyClientRegistrationCommand(
       [command, ...args],
@@ -1183,8 +1171,5 @@ const uninstallStatusPriority = (status: UninstallItem["status"]): number => {
     }
   }
 };
-const registrationSchema = z
-  .object({ command: z.string(), args: z.array(z.string()) })
-  .passthrough();
 const isMissing = (cause: unknown): boolean =>
   cause instanceof Error && "code" in cause && cause.code === "ENOENT";
diff --git a/tests/boundary/cli/cliSetup.test.ts b/tests/boundary/cli/cliSetup.test.ts
index 15cea67f50..00e45c5b17 100644
--- a/tests/boundary/cli/cliSetup.test.ts
+++ b/tests/boundary/cli/cliSetup.test.ts
@@ -9,14 +9,16 @@ import {
   symlink,
   writeFile,
 } from "node:fs/promises";
-import { dirname, join } from "node:path";
+import { dirname, join, resolve } from "node:path";
 import { promisify } from "node:util";
 
 import { spawn } from "@lydell/node-pty";
 import { describe, expect, it } from "vitest";
 import { z } from "zod";
+import { parse as parseToml } from "smol-toml";
 
 import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { cliTest } from "../../support/cli/cliFixture.js";
 
 const execute = promisify(execFile);
 const decisionMarker = "REA_SETUP_DECISION:";
@@ -176,6 +178,107 @@ describe("TTY setup dry run", () => {
   });
 });
 
+cliTest.skipIf(process.platform === "win32")(
+  "repairs a Codex timeout without replacing an equivalent caller-selected launcher",
+  async ({ cli }) => {
+    const home = await createTestTempDirectory("rea-codex-alias-repair-");
+    const codexHome = join(home, ".codex");
+    const config = join(codexHome, "config.toml");
+    const backup = `${config}.rea.backup`;
+    const alias = join(home, "rea-launcher-alias.mjs");
+    await mkdir(codexHome);
+    await symlink(resolve("scripts/rea.mjs"), alias, "file");
+    const original = [
+      "# Caller-owned Codex approval policy",
+      'approval_policy = "on-request"',
+      'sandbox_mode = "read-only"',
+      "",
+      "[mcp_servers.rea]",
+      `command = ${JSON.stringify(process.execPath)}`,
+      `args = ${JSON.stringify([alias, "mcp"])}`,
+      "startup_timeout_sec = 0",
+      "tool_timeout_sec = 900",
+      'default_tools_approval_mode = "prompt"',
+      "",
+      "[mcp_servers.rea.tools.open_binary]",
+      'approval_mode = "approve"',
+      "output_token_limit = 2048",
+      "",
+    ].join("\n");
+    await writeFile(config, original);
+    const setup = (approval: "--dry-run" | "--yes") =>
+      cli.run({
+        arguments: [
+          "setup",
+          "--client",
+          "codex",
+          "--no-skill",
+          approval,
+          "--json",
+        ],
+        cwd: home,
+        environment: {
+          HOME: home,
+          USERPROFILE: home,
+          CODEX_HOME: codexHome,
+          XDG_CONFIG_HOME: join(home, ".config"),
+          XDG_DATA_HOME: join(home, ".local", "share"),
+          XDG_CACHE_HOME: join(home, ".cache"),
+        },
+        timeoutMs: 20_000,
+      });
+
+    const planned = await setup("--dry-run");
+    expect(planned.exitCode, planned.stderr).toBe(0);
+    expect(planned.json).toMatchObject({
+      status: "planned",
+      plannedActions: [
+        expect.objectContaining({
+          id: "configure_client:codex",
+          operation: "update",
+          target: config,
+          backupPath: backup,
+        }),
+      ],
+    });
+    expect(await readFile(config, "utf8")).toBe(original);
+    await expect(access(backup)).rejects.toMatchObject({ code: "ENOENT" });
+
+    const applied = await setup("--yes");
+    expect(applied.exitCode, applied.stderr).toBe(0);
+    expect(applied.json).toMatchObject({ status: "ready" });
+    const repaired = await readFile(config, "utf8");
+    expect(parseToml(repaired)).toMatchObject({
+      approval_policy: "on-request",
+      sandbox_mode: "read-only",
+      mcp_servers: {
+        rea: {
+          command: process.execPath,
+          args: [alias, "mcp"],
+          startup_timeout_sec: 30,
+          tool_timeout_sec: 900,
+          default_tools_approval_mode: "prompt",
+          tools: {
+            open_binary: { approval_mode: "approve", output_token_limit: 2048 },
+          },
+        },
+      },
+    });
+    expect(await readFile(backup, "utf8")).toBe(original);
+    expect((await lstat(alias)).isSymbolicLink()).toBe(true);
+
+    const repeated = await setup("--yes");
+    expect(repeated.exitCode, repeated.stderr).toBe(0);
+    expect(repeated.json).toMatchObject({
+      status: "ready",
+      plannedActions: [],
+      appliedActions: [],
+    });
+    expect(await readFile(config, "utf8")).toBe(repaired);
+    expect(await readFile(backup, "utf8")).toBe(original);
+  },
+);
+
 describe("interactive setup journey", () => {
   it("shows detected and absent clients without preselecting detected clients", async () => {
     const result = await runJourney(
diff --git a/tests/boundary/filesystem/clientRegistrationOwnership.test.ts b/tests/boundary/filesystem/clientRegistrationOwnership.test.ts
new file mode 100644
index 0000000000..efc85ad9aa
--- /dev/null
+++ b/tests/boundary/filesystem/clientRegistrationOwnership.test.ts
@@ -0,0 +1,155 @@
+import { mkdir, readFile, readdir, writeFile } from "node:fs/promises";
+import { dirname, join } from "node:path";
+
+import { parse as parseToml } from "smol-toml";
+import { expect, it } from "vitest";
+
+import { readClientRegistrationStatuses } from "../../../src/application/ClientRegistrationStatus.js";
+import { systemUninstallHost } from "../../../src/application/Uninstall.js";
+import { PRODUCT_IDENTITY } from "../../../src/identity.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+
+const codexSource = (invalid: string): string =>
+  [
+    'caller_root = "keep"',
+    "[mcp_servers.rea]",
+    `command = "${PRODUCT_IDENTITY.cliBinary}"`,
+    'args = ["mcp"]',
+    invalid,
+    "[mcp_servers.peer]",
+    'command = "peer"',
+    "args = []",
+    "",
+  ].join("\n");
+
+it.each([
+  {
+    client: "codex",
+    path: ".codex/config.toml",
+    invalid: "invalid tool policy",
+    source: codexSource('enabled_tools = "not-an-array"'),
+    parse: (text: string): unknown => parseToml(text),
+    remaining: {
+      caller_root: "keep",
+      mcp_servers: { peer: { command: "peer", args: [] } },
+    },
+  },
+  {
+    client: "codex",
+    path: ".codex/config.toml",
+    invalid: "a nonpositive startup timeout",
+    source: codexSource("startup_timeout_sec = 0"),
+    parse: (text: string): unknown => parseToml(text),
+    remaining: {
+      caller_root: "keep",
+      mcp_servers: { peer: { command: "peer", args: [] } },
+    },
+  },
+  {
+    client: "opencode",
+    path: ".config/opencode/opencode.json",
+    invalid: "a non-string environment value",
+    source: JSON.stringify({
+      caller_root: "keep",
+      mcp: {
+        servers: {
+          rea: {
+            type: "local",
+            command: [PRODUCT_IDENTITY.cliBinary, "mcp"],
+            environment: { CALLER_SETTING: 42 },
+          },
+          peer: { type: "local", command: ["peer"] },
+        },
+      },
+    }),
+    parse: (text: string): unknown => JSON.parse(text),
+    remaining: {
+      caller_root: "keep",
+      mcp: { servers: { peer: { type: "local", command: ["peer"] } } },
+    },
+  },
+])(
+  "removes the owned $client registration despite $invalid",
+  async (sample) => {
+    const home = await createTestTempDirectory("rea-registration-ownership-");
+    const configPath = join(home, sample.path);
+    const environment = {
+      CODEX_HOME: join(home, ".codex"),
+      XDG_CONFIG_HOME: join(home, ".config"),
+    };
+    await mkdir(dirname(configPath), { recursive: true });
+    await writeFile(configPath, sample.source);
+    const statuses = await readClientRegistrationStatuses(home, undefined, {
+      environment,
+    });
+    expect(
+      statuses.find(({ client }) => client === sample.client),
+    ).toMatchObject({
+      state: "invalid",
+    });
+    const host = systemUninstallHost(home, undefined, environment);
+    try {
+      const client = (await host.clients()).find(
+        (client) =>
+          client.name === sample.client && client.configPath === configPath,
+      );
+      if (client === undefined)
+        throw new Error("Expected the configured client");
+      expect(await host.removeClient(client)).toMatchObject({
+        name: sample.client,
+        status: "removed",
+      });
+      expect(sample.parse(await readFile(configPath, "utf8"))).toEqual(
+        sample.remaining,
+      );
+      expect(await readFile(`${configPath}.rea.backup`, "utf8")).toBe(
+        sample.source,
+      );
+    } finally {
+      expect(await host.close?.()).toBeUndefined();
+    }
+  },
+);
+
+it("retains an OpenCode remote registration with a REA-like command", async () => {
+  const home = await createTestTempDirectory("rea-registration-remote-owner-");
+  const configPath = join(home, ".config/opencode/opencode.json");
+  const environment = { XDG_CONFIG_HOME: join(home, ".config") };
+  const source = JSON.stringify({
+    caller_root: "keep",
+    mcp: {
+      servers: {
+        rea: {
+          type: "remote",
+          url: "https://caller.example/mcp",
+          command: [PRODUCT_IDENTITY.cliBinary, "mcp"],
+        },
+        peer: { type: "local", command: ["peer"] },
+      },
+    },
+  });
+  await mkdir(dirname(configPath), { recursive: true });
+  await writeFile(configPath, source);
+  const statuses = await readClientRegistrationStatuses(home, undefined, {
+    environment,
+  });
+  expect(statuses.find(({ client }) => client === "opencode")).toMatchObject({
+    state: "invalid",
+  });
+  const host = systemUninstallHost(home, undefined, environment);
+  try {
+    const client = (await host.clients()).find(
+      (client) =>
+        client.name === "opencode" && client.configPath === configPath,
+    );
+    if (client === undefined) throw new Error("Expected the configured client");
+    expect(await host.removeClient(client)).toMatchObject({
+      name: "opencode",
+      status: "retained",
+    });
+    expect(await readFile(configPath, "utf8")).toBe(source);
+    expect(await readdir(dirname(configPath))).toEqual(["opencode.json"]);
+  } finally {
+    expect(await host.close?.()).toBeUndefined();
+  }
+});
diff --git a/tests/boundary/filesystem/setupConfig.test.ts b/tests/boundary/filesystem/setupConfig.test.ts
index 91bbff9301..ea21eec1b3 100644
--- a/tests/boundary/filesystem/setupConfig.test.ts
+++ b/tests/boundary/filesystem/setupConfig.test.ts
@@ -9,6 +9,7 @@ import {
 } from "node:fs/promises";
 import { join } from "node:path";
 import { describe, expect, it } from "vitest";
+import { parse as parseToml } from "smol-toml";
 
 import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
 
@@ -69,6 +70,57 @@ it.skipIf(process.platform === "win32")(
   },
 );
 
+it.skipIf(process.platform === "win32")(
+  "repairs a Codex timeout without replacing an equivalent caller launcher alias",
+  async () => {
+    const home = await createTestTempDirectory(
+      "rea-config-timeout-launcher-alias-",
+    );
+    const real = join(home, "rea-current");
+    const alias = join(home, "rea-alias");
+    await writeFile(real, "current launcher\n");
+    await symlink(real, alias);
+    await mkdir(join(home, ".codex"));
+    const configPath = join(home, ".codex", "config.toml");
+    const original = [
+      "[mcp_servers.rea]",
+      `command = ${JSON.stringify(alias)}`,
+      'args = ["mcp"]',
+      "startup_timeout_sec = 0",
+      "tool_timeout_sec = 450",
+      "future_policy = { retain = true }",
+      "",
+      "[mcp_servers.rea.env]",
+      'CALLER_SETTING = "keep exactly"',
+      "",
+    ].join("\n");
+    await writeFile(configPath, original);
+    const client = { name: "codex", format: "toml", configPath } as const;
+    expect(
+      await configureClientConfiguration(client, {}, [real, "mcp"]),
+    ).toMatchObject({ status: "configured" });
+    const configured = await readFile(configPath, "utf8");
+    expect(parseToml(configured)).toMatchObject({
+      mcp_servers: {
+        rea: {
+          command: alias,
+          args: ["mcp"],
+          startup_timeout_sec: 30,
+          tool_timeout_sec: 450,
+          future_policy: { retain: true },
+          env: { CALLER_SETTING: "keep exactly" },
+        },
+      },
+    });
+    expect(await readFile(`${configPath}.rea.backup`, "utf8")).toBe(original);
+    expect(
+      await configureClientConfiguration(client, {}, [real, "mcp"]),
+    ).toEqual({ status: "unchanged" });
+    expect(await readFile(configPath, "utf8")).toBe(configured);
+    expect(await readFile(`${configPath}.rea.backup`, "utf8")).toBe(original);
+  },
+);
+
 describe("JSON client configuration transaction: writing configuration through safe paths", () => {
   it.skipIf(typeof process.getuid !== "function")(
     "rejects a symlink target not owned by the current user",