fix(setup): match retained fields to the client that writes them

Codex drops a tools array that its stdio config rejects, and the Harness approval plan lists the Cordis launcher keys the writer replaces.

docs/installation.md

@@ -68,9 +68,12 @@ client-specific keys. It removes remote-server keys such as `url`, `headers`,
 `enabled: false` or (outside Grok Build) `disabled: true`, so the registration
 is active. A registration field that does not parse, including a non-boolean
 `enabled` or `disabled` and a malformed `startup_timeout_sec` or `tools`, is
-removed too. An existing entry without a
-`command` is a remote server and is replaced whole. A legacy OpenCode entry
-moved into the native `mcp.servers` table keeps only its environment.
+removed too. A `tools` value is removed except on GitHub Copilot CLI, which
+replaces it with `["*"]`; Codex rejects a `tools` sequence. An existing entry
+without a `command` is a remote server and is replaced whole. DeepSeek Harness
+keeps other fields on the existing Cordis server and replaces `serverName`,
+`transport`, `command`, and `args`. A legacy OpenCode entry moved into the
+native `mcp.servers` table keeps only its environment.
 Setup and doctor report a malformed REA environment map or invalid runtime
 setting before setup writes files. Repair the named setting in the client
 configuration; setup does not silently discard the rest of the map.

src/application/ClientConfigurationDocument.ts

@@ -1536,6 +1536,13 @@ const REGISTRATION_REMOTE_KEYS: Readonly<Record<string, true>> = {
 const keepsGrokDisabledFlag = (dialect: ClientRegistrationDialect): boolean =>
   dialect === "grok";
 
+/**
+ * Copilot rewrites `tools` as a string array. Other clients do not: Codex
+ * expects a map and rejects a sequence (`invalid type: sequence, expected a map`).
+ */
+const keepsCopilotTools = (dialect: ClientRegistrationDialect): boolean =>
+  dialect === "copilot_cli";
+
 /**
  * Whether setup replaces or removes an existing entry key. Setup registers an
  * active server, so entry-level switches that turn it off are removed too.
@@ -1551,6 +1558,7 @@ const registrationManagedKey = (
   Object.hasOwn(REGISTRATION_LAUNCHER_KEYS, key) ||
   Object.hasOwn(REGISTRATION_REMOTE_KEYS, key) ||
   !registrationFieldAccepted(key, value) ||
+  (key === "tools" && !keepsCopilotTools(dialect)) ||
   (key === "enabled" && value === false) ||
   (key === "disabled" && value === true && !keepsGrokDisabledFlag(dialect));
 
@@ -1613,10 +1621,11 @@ export const describeClientRegistrationRetention = (
   const removed = keepsGrokDisabledFlag(dialect)
     ? "Remote-server keys, an enabled: false switch, and registration fields that do not parse are removed. A boolean disabled value is kept."
     : "Remote-server keys, switches that turn the server off, and registration fields that do not parse are removed.";
+  const tools = keepsCopilotTools(dialect) ? "" : " A tools value is removed.";
   const replacement =
     replaced.length === 0
-      ? removed
-      : `Setup replaces ${replaced.join(" and ")}. ${removed}`;
+      ? `${removed}${tools}`
+      : `Setup replaces ${replaced.join(" and ")}. ${removed}${tools}`;
   const legacy =
     dialect === "opencode_v2"
       ? " A legacy OpenCode entry moved into the native server table keeps only its environment."

src/application/DshCordisPatch.ts

@@ -404,6 +404,18 @@ export const serializeDshDocument = (
     throw new ConfigurationError("Missing Cordis edit plan");
   return document.cordis.source.serialize(document.cordis.desired);
 };
+/** Approval-plan text for the launcher keys `DshCordisDocument` replaces. */
+export const describeDshRegistrationRetention = (
+  command: readonly string[],
+): string => {
+  const entry = dshClientRegistrationEntry(command);
+  const replaced = [...LAUNCHER_KEYS]
+    .filter((key) => Object.hasOwn(entry, key))
+    .sort((left, right) => left.localeCompare(right))
+    .map((key) => `${key} with ${JSON.stringify(entry[key])}`);
+  return `Other fields on the existing Cordis server are kept. Setup replaces ${replaced.join(", ")}. Environment overrides are merged.`;
+};
+
 export const dshClientRegistrationEntry = (
   command: readonly string[],
   environment: Readonly<Record<string, string>> = {},

src/application/Setup.planning.test.ts

@@ -159,6 +159,9 @@ describe("setup workflow", () => {
     expect(result.plannedActions[0]?.detail).toContain(
       "registration fields that do not parse are removed",
     );
+    expect(result.plannedActions[0]?.detail).toContain(
+      "A tools value is removed.",
+    );
     expect(host.hopperInstalls).toBe(0);
     expect(host.configurations).toBe(0);
   });
@@ -270,6 +273,36 @@ describe("setup approval disclosure", () => {
     );
     expect(detail).not.toContain(`enabled with ${JSON.stringify(true)}`);
   });
+
+  it("describes Cordis fields the Harness writer replaces", async () => {
+    const host = new FakeSetupHost();
+    host.hopper = "/Applications/Hopper";
+    host.skill = "unchanged";
+    host.clients = [
+      {
+        name: "dsh",
+        displayName: "DeepSeek Harness",
+        configPath: "/cordis.patch.yml",
+        format: "dsh",
+      },
+    ];
+
+    const result = await runSetup(
+      { ...options(false), dryRun: true, clientIds: ["dsh"] },
+      host,
+    );
+    const detail = result.plannedActions[0]?.detail ?? "";
+    const [executable = "rea", ...args] = host.registrationCommand;
+
+    expect(detail).toContain(
+      "Other fields on the existing Cordis server are kept.",
+    );
+    expect(detail).toContain(`serverName with ${JSON.stringify("rea")}`);
+    expect(detail).toContain(`transport with ${JSON.stringify("stdio")}`);
+    expect(detail).toContain(`command with ${JSON.stringify(executable)}`);
+    expect(detail).toContain(`args with ${JSON.stringify(args)}`);
+    expect(detail).not.toContain("Remote-server keys");
+  });
 });
 
 describe("setup workflow lifecycle and provider planning", () => {

src/application/SetupPlan.ts

@@ -4,6 +4,7 @@ import {
   describeClientRegistrationRetention,
   type ClientRegistrationDialect,
 } from "./ClientConfigurationDocument.js";
+import { describeDshRegistrationRetention } from "./DshCordisPatch.js";
 import { isOwnedClientRegistrationCommand } from "./ClientRegistrationIdentity.js";
 import {
   linuxHopperInstallDisclosure,
@@ -334,10 +335,10 @@ const clientConfigurationDetail = (
     (client.format === undefined || client.format === "unsupported"
       ? "json"
       : client.format);
-  const retainedFields = describeClientRegistrationRetention(
-    client.name,
-    dialect,
-  );
+  const retainedFields =
+    dialect === "dsh"
+      ? describeDshRegistrationRetention(command)
+      : describeClientRegistrationRetention(client.name, dialect);
   const environmentDetail =
     entries.length === 0
       ? ` No additional provider environment variables. Existing server environment overrides are retained. ${retainedFields}`

tests/boundary/filesystem/clientRegistrationFields.test.ts

@@ -139,6 +139,32 @@ it("drops Codex oauth_resource from a local command entry", async () => {
   });
 });
 
+it("drops a Codex tools array from a local command entry", async () => {
+  const root = await createTestTempDirectory("rea-registration-codex-tools-");
+  const configPath = join(root, "config.toml");
+  const client: SetupClient = { name: "codex", format: "toml", configPath };
+  const existing = {
+    ...clientRegistrationEntry("toml", ["rea-old", "mcp"], environment),
+    tool_timeout_sec: 900,
+    tools: ["*"],
+  };
+  await writeFile(
+    configPath,
+    serializeClientConfiguration(configurationWith("toml", existing), "toml"),
+  );
+  expect(await configureClientConfiguration(client, {}, command)).toMatchObject(
+    { status: "configured" },
+  );
+  expect(
+    parseClientConfiguration(await readFile(configPath, "utf8"), "toml").servers
+      .rea,
+  ).toEqual({
+    ...clientRegistrationEntry("toml", command, environment),
+    startup_timeout_sec: MCP_STARTUP_POLICY.codexStartupTimeoutSeconds,
+    tool_timeout_sec: 900,
+  });
+});
+
 it("drops malformed registration fields from a local command entry", async () => {
   const root = await createTestTempDirectory("rea-registration-schema-");
   const configPath = join(root, "mcp.json");