fix(uninstall): remove the REA-owned ZCode fallback registration (#2783)

* fix(uninstall): remove the REA-owned ZCode fallback registration

ZCode loads the user-scope `~/.agents/mcp.json` `mcpServers` fallback
whenever its native `mcp.servers` table is empty. Uninstall removed REA
only from the native table, so a REA-owned fallback entry became eligible
to load again once the last native server was gone, while uninstall
reported ZCode as removed and complete.

Also visit the ZCode fallback as a standard `mcpServers` JSON
configuration in the uninstall host. It goes through the same
ownership check, `.rea.backup`, readback and restore path as every other
client configuration, so other fallback servers and settings, and a
foreign `rea` entry, are preserved. Its result merges into the ZCode item.

Fixes #2664

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(uninstall): preserve the strict ZCode fallback dialect

Address review findings at their producing boundaries and preserve directly affected consumers. Source inspection and git diff --check completed. Tests and automated checks were not run at the user’s explicit request.

* fix(comparison): recheck historical calls-only changes (#2223)

* fix(comparison): preserve incomplete function call evidence

Keep missing, unknown, partial and unresolved call relationships unknown in function comparisons and reconstruction claims. Aggregate IDA caller and callee coverage without overwriting uncertainty.

Validate with 144 focused tests, typecheck/lint, docs checks and test discovery. Real providers were not verified; the full headless IDA session suite requires unavailable Windows native controls.

* fix(comparison): recheck historical calls-only changes

---------

Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>

* fix(ci): isolate Linux Hopper process fixture inventory

* fix(android): make DEX descriptor pattern portable

* fix: repair the static-check failures on the default branch (#2895)

* fix: repair the static-check failures on the default branch

The default branch fails its own required `Static checks` job three ways, so
every pull request reports that job as failed regardless of its own change.

- `npm run format:check` reports `src/domain/functionComparison.test.ts` and
  `src/ida/IdaOperationRunner.ts`.
- `npm run lint` reports a duplicate `import { join } from "node:path"` in
  `tests/boundary/mcp/ghidraInventoryMcp.test.ts` (lines 4 and 17).
- `npm run typecheck` reports `format: "devin"` missing from the client format
  union in `src/application/SupportedClients.ts`, and an unchecked index in
  `tests/boundary/cli/clientProfileLifecycle.test.ts`, whose pair array is
  inferred as `string[][]`.

Apply the pinned formatter, drop the duplicate import, list the `"devin"` format
that its own definition already uses, and mark the pair array `as const`.

Validation: `npm run check:fast` and `npm run format:check` pass.

* fix(setup): keep Devin on the JSON configuration dialect

---------

Co-authored-by: 吴佳浩 <wujiahao@supremind.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Co-authored-by: Lucien <164857476+dakjdakd@users.noreply.github.com>
Co-authored-by: 吴佳浩Alben <35291372+XiaoBinGan@users.noreply.github.com>
Co-authored-by: 吴佳浩 <wujiahao@supremind.com>

docs/client-configuration.md

@@ -294,7 +294,11 @@ the first native server into an empty table, it copies the fallback's
 `mcpServers` entries into the native table so they keep loading, and leaves
 the fallback file untouched. Existing REA environment overrides are preserved
 when refreshing its command. A malformed or unreadable fallback file fails setup instead of
-being silently suppressed; repair or remove it and rerun. ZCode disables a
+being silently suppressed; repair or remove it and rerun. Uninstall removes an
+REA-owned `rea` entry from both the native table and the fallback, backing up
+each changed file, so an emptied native table cannot load a leftover fallback
+registration; other fallback servers, settings and a foreign `rea` entry are
+kept. ZCode disables a
 server with `enable: false` on its entry; doctor reports such a registration
 as stale, and rerunning setup removes the flag to repair it. Native configuration
 uses strict JSON; setup refuses comments, trailing commas and a BOM rather than

src/application/ClientConfigurationDocument.ts

@@ -167,7 +167,7 @@ export const parseZcodeFallbackConfiguration = (
         ? {}
         : requireObject(document.mcpServers, "ZCode fallback mcpServers"),
     serversPath: ["mcpServers"],
-    dialect: "json",
+    dialect: "zcode_fallback",
     legacyServers: {},
   };
 };
@@ -183,6 +183,7 @@ export const parseClientConfiguration = (
   if (format === undefined || format === "unsupported")
     throw new TypeError("client does not have a supported MCP config format");
   // DeepSeek Harness stores a Cordis patch list, not a server table.
+  if (format === "zcode_fallback") return parseZcodeFallbackConfiguration(text);
   if (format === "dsh") return parseDshCordisDocument(text);
   const document = parseDocument(text, format);
   const serversKey = clientConfigurationServersKey(format);

src/application/SupportedClients.ts

@@ -47,6 +47,7 @@ export interface SetupClient {
     | "pi"
     | "kimi"
     | "hermes"
+    | "zcode_fallback"
     | "zcode"
     | "dsh"
     | "unsupported";

src/application/Uninstall.ts

@@ -231,12 +231,21 @@ export const systemUninstallHost = (
       const clients = supportedClients(home, platform, environment);
       redirection = appDataRedirection(clients);
       return Promise.resolve(
-        clients.flatMap((client) =>
-          uninstallConfigPaths(client).map((configPath) => ({
+        clients.flatMap((client) => [
+          ...uninstallConfigPaths(client).map((configPath) => ({
             ...client,
             configPath,
           })),
-        ),
+          ...(client.zcodeFallbackPath === undefined
+            ? []
+            : [
+                {
+                  ...client,
+                  configPath: client.zcodeFallbackPath,
+                  format: "zcode_fallback" as const,
+                },
+              ]),
+        ]),
       );
     },
     inspectClient: async (client) => {

tests/boundary/filesystem/zcodeClientConfiguration.test.ts

@@ -13,7 +13,10 @@ import {
 } from "../../../src/application/SetupClientConfiguration.js";
 import { skillDestinations } from "../../../src/application/SetupSkill.js";
 import { supportedClients } from "../../../src/application/SupportedClients.js";
-import { systemUninstallHost } from "../../../src/application/Uninstall.js";
+import {
+  runUninstall,
+  systemUninstallHost,
+} from "../../../src/application/Uninstall.js";
 import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
 import { clearClientLocationEnvironment } from "../../fixtures/clientEnvironment.js";
 
@@ -257,6 +260,91 @@ describe("ZCode .agents fallback preservation", () => {
   });
 });
 
+describe("ZCode fallback uninstall", () => {
+  const owned = { command: command[0], args: command.slice(1) };
+  const writeFallback = async (home: string, servers: object) => {
+    await mkdir(join(home, ".agents"), { recursive: true });
+    const text = `${JSON.stringify({ ui: { keep: true }, mcpServers: servers }, null, 2)}\n`;
+    await writeFile(fallbackPath(home), text);
+    return text;
+  };
+
+  it.each(["comment", "trailing-comma", "bom"])(
+    "fails closed on strict fallback syntax: %s",
+    async (mode) => {
+      const { home } = await zcodeClient();
+      const valid = await writeFallback(home, {
+        rea: owned,
+        other: { command: "other-server" },
+      });
+      const original =
+        mode === "comment"
+          ? `// unsupported comment\n${valid}`
+          : mode === "bom"
+            ? `\uFEFF${valid}`
+            : valid.replace(/\}\s*$/u, ",}");
+      await writeFile(fallbackPath(home), original);
+      const result = await runUninstall(false, systemUninstallHost(home));
+      expect(result.items).toContainEqual(
+        expect.objectContaining({ name: "zcode", status: "failed" }),
+      );
+      expect(await readFile(fallbackPath(home), "utf8")).toBe(original);
+      await expect(
+        readFile(`${fallbackPath(home)}.rea.backup`),
+      ).rejects.toMatchObject({ code: "ENOENT" });
+    },
+  );
+
+  it("removes the REA-owned fallback entry with the native registration", async () => {
+    const { home, client } = await zcodeClient();
+    await writeFile(
+      client.configPath,
+      JSON.stringify({ mcp: { servers: { rea: owned } } }),
+    );
+    const original = await writeFallback(home, {
+      rea: owned,
+      other: { command: "other-server" },
+    });
+
+    const result = await runUninstall(false, systemUninstallHost(home));
+
+    expect(result.status).toBe("complete");
+    expect(result.items.find(({ name }) => name === "zcode")?.status).toBe(
+      "removed",
+    );
+    const native = JSON.parse(await readFile(client.configPath, "utf8"));
+    expect(native.mcp.servers).toEqual({});
+    const fallback = JSON.parse(await readFile(fallbackPath(home), "utf8"));
+    expect(fallback).toEqual({
+      ui: { keep: true },
+      mcpServers: { other: { command: "other-server" } },
+    });
+    expect(await readFile(`${fallbackPath(home)}.rea.backup`, "utf8")).toBe(
+      original,
+    );
+  });
+
+  it("removes a fallback-only REA entry and keeps a foreign rea entry", async () => {
+    for (const [servers, expected] of [
+      [{ rea: owned }, {}],
+      [
+        { rea: { command: "someone-else" } },
+        { rea: { command: "someone-else" } },
+      ],
+    ] as const) {
+      const { home } = await zcodeClient();
+      await writeFallback(home, servers);
+
+      expect(
+        (await runUninstall(false, systemUninstallHost(home))).status,
+      ).toBe("complete");
+      expect(
+        JSON.parse(await readFile(fallbackPath(home), "utf8")).mcpServers,
+      ).toEqual(expected);
+    }
+  });
+});
+
 describe("ZCode fallback admission", () => {
   it.each([{ PORT: 123 }, { REA_MCP_INPUT_SCHEMA_PROFILE: "unknown" }])(
     "refuses malformed fallback REA environment %j before native writes",