diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f3216a4d3..0e8ab1d7c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,6 +53,9 @@ jobs:
           ARCHITECTURE_BASE: ${{ github.event.pull_request.base.sha || github.event.before || 'HEAD^' }}
         run: node scripts/check-architecture.mjs
 
+      - name: Unit-test the Pi patch checks
+        run: node --test scripts/pi-patch-hash.test.mjs
+
       - name: Unit tests
         run: pnpm -r --if-present test
 
diff --git a/packages/agent-runtime/src/native-pi-session.test.ts b/packages/agent-runtime/src/native-pi-session.test.ts
index 43bc90963..770b3c1dd 100644
--- a/packages/agent-runtime/src/native-pi-session.test.ts
+++ b/packages/agent-runtime/src/native-pi-session.test.ts
@@ -1,6 +1,6 @@
 import { existsSync, mkdtempSync, mkdirSync, readFileSync, readdirSync, realpathSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
-import { join } from "node:path";
+import { basename, join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 import { AgentSession, ModelRuntime, SessionManager } from "@earendil-works/pi-coding-agent";
 import { createAssistantMessageEventStream, type AssistantMessage } from "@earendil-works/pi-ai";
@@ -799,7 +799,7 @@ describe("native fork children", () => {
         expect(failure?.message).not.toContain(f.group);
         expect(existsSync(foreignPath)).toBe(true);
         expect(readFileSync(foreignPath, "utf8")).toContain("collision");
-        expect(groupEntries(f.group).sort()).toEqual(before.concat([foreignPath.split("/").at(-1)!]).sort());
+        expect(groupEntries(f.group).sort()).toEqual(before.concat([basename(foreignPath)]).sort());
         expect(readFileSync(f.file, "utf8")).toBe(parentBytes);
       } finally { service.disposeAll(); }
     } finally {
diff --git a/scripts/check-pi-dependencies.mjs b/scripts/check-pi-dependencies.mjs
index c31cc6acf..0f03ac6ae 100644
--- a/scripts/check-pi-dependencies.mjs
+++ b/scripts/check-pi-dependencies.mjs
@@ -1,8 +1,30 @@
+#!/usr/bin/env node
+/**
+ * Require every pinned Pi package to be installed at the target version, and
+ * the ones we patch to be installed as pnpm's patched instance.
+ *
+ * Usage:
+ *   node scripts/check-pi-dependencies.mjs
+ *   node scripts/check-pi-dependencies.mjs --root <dir>
+ *   pnpm check:pi-dependencies
+ */
 import { existsSync, readFileSync, realpathSync } from "node:fs";
 import { dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
+import { installedPatchHashes } from "./pi-patch-hash.mjs";
 
-const root = resolve(dirname(fileURLToPath(import.meta.url)), "..");
+function parseArgs(argv) {
+  let out = resolve(dirname(fileURLToPath(import.meta.url)), "..");
+  for (let i = 0; i < argv.length; i += 1) {
+    if (argv[i] === "--root" && argv[i + 1]) {
+      out = resolve(argv[i + 1]);
+      i += 1;
+    }
+  }
+  return out;
+}
+
+const root = parseArgs(process.argv.slice(2));
 const targetVersion = "1.0.1";
 
 function readJson(path) {
@@ -25,7 +47,7 @@ function assertInstalled(packagePath, expectedName, { patched = false } = {}) {
   if (manifest.name !== expectedName || manifest.version !== targetVersion) {
     throw new Error(`${packagePath} resolves to ${manifest.name}@${manifest.version}, expected ${expectedName}@${targetVersion}`);
   }
-  if (patched && !resolved.includes("patch_hash=")) {
+  if (patched && installedPatchHashes(root, expectedName, targetVersion).length === 0) {
     throw new Error(`${packagePath} does not resolve to pnpm's patched package instance`);
   }
 }
diff --git a/scripts/check-pi-patches.mjs b/scripts/check-pi-patches.mjs
index 2164f4f81..6e56f3c71 100644
--- a/scripts/check-pi-patches.mjs
+++ b/scripts/check-pi-patches.mjs
@@ -1,8 +1,30 @@
-import { existsSync, readFileSync, realpathSync } from "node:fs";
+#!/usr/bin/env node
+/**
+ * Require every Pi patch to be mapped in pnpm-workspace.yaml, installed by
+ * pnpm, recorded in pnpm-lock.yaml, and to still carry the audited contracts.
+ *
+ * Usage:
+ *   node scripts/check-pi-patches.mjs
+ *   node scripts/check-pi-patches.mjs --root <dir>
+ *   pnpm check:pi-patches
+ */
+import { existsSync, readFileSync } from "node:fs";
 import { dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
+import { installedPatchHashes } from "./pi-patch-hash.mjs";
 
-const root = resolve(dirname(fileURLToPath(import.meta.url)), "..");
+function parseArgs(argv) {
+  let out = resolve(dirname(fileURLToPath(import.meta.url)), "..");
+  for (let i = 0; i < argv.length; i += 1) {
+    if (argv[i] === "--root" && argv[i + 1]) {
+      out = resolve(argv[i + 1]);
+      i += 1;
+    }
+  }
+  return out;
+}
+
+const root = parseArgs(process.argv.slice(2));
 const targetVersion = "1.0.1";
 const entries = [
   {
@@ -39,10 +61,20 @@ for (const entry of entries) {
   const workspaceMapping = `'${entry.name}@${targetVersion}': ${entry.patch}`;
   if (!workspace.includes(workspaceMapping)) throw new Error(`pnpm-workspace.yaml does not map ${entry.name} to ${entry.patch}`);
   const packagePath = join(root, entry.packagePath);
-  const resolved = realpathSync(packagePath);
-  const patchHash = resolved.match(/patch_hash=([a-f0-9]+)/)?.[1];
-  if (!patchHash || !lockfile.includes(`${entry.name}@${targetVersion}(patch_hash=${patchHash}`)) {
-    throw new Error(`${entry.name}@${targetVersion} installed patch hash is absent from pnpm-lock.yaml`);
+  if (!existsSync(packagePath)) {
+    throw new Error(`Install dependencies before this check; missing ${entry.packagePath}`);
+  }
+  const patchHashes = installedPatchHashes(root, entry.name, targetVersion);
+  if (patchHashes.length === 0) {
+    throw new Error(`${entry.name}@${targetVersion} is not installed as a patched instance`);
+  }
+  const unlocked = patchHashes.filter(
+    (patchHash) => !lockfile.includes(`${entry.name}@${targetVersion}(patch_hash=${patchHash}`),
+  );
+  if (unlocked.length > 0) {
+    throw new Error(
+      `${entry.name}@${targetVersion} installed patch hash is absent from pnpm-lock.yaml: ${unlocked.join(", ")}`,
+    );
   }
 }
 
diff --git a/scripts/pi-patch-hash.mjs b/scripts/pi-patch-hash.mjs
new file mode 100644
index 000000000..5a18bfbc5
--- /dev/null
+++ b/scripts/pi-patch-hash.mjs
@@ -0,0 +1,36 @@
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+
+/**
+ * pnpm copies the lockfile it actually installed from into the virtual
+ * store, next to the store entries it describes.
+ */
+export const VIRTUAL_STORE_LOCKFILE = join("node_modules", ".pnpm", "lock.yaml");
+
+function escapeForRegExp(value) {
+  return value.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+}
+
+/**
+ * Return the patch hashes pnpm recorded for `name@version` in a lockfile.
+ *
+ * Every patched snapshot is keyed `'name@version(patch_hash=<hex>)...`
+ * (single-quoted for scoped names, bare otherwise), so the snapshot keys
+ * carry the full hash even when the matching `.pnpm` directory name has
+ * been shortened.
+ */
+export function patchHashesIn(lockText, name, version) {
+  const snapshotKey = new RegExp(
+    `'?${escapeForRegExp(name)}@${escapeForRegExp(version)}\\(patch_hash=([a-f0-9]+)\\)`,
+    "g",
+  );
+  return [...new Set([...lockText.matchAll(snapshotKey)].map((match) => match[1]))].sort();
+}
+
+/**
+ * Patch hashes of the instances pnpm actually installed, read from the
+ * virtual store's own lockfile.
+ */
+export function installedPatchHashes(root, name, version) {
+  return patchHashesIn(readFileSync(join(root, VIRTUAL_STORE_LOCKFILE), "utf8"), name, version);
+}
\ No newline at end of file
diff --git a/scripts/pi-patch-hash.test.mjs b/scripts/pi-patch-hash.test.mjs
new file mode 100644
index 000000000..60dda0cc8
--- /dev/null
+++ b/scripts/pi-patch-hash.test.mjs
@@ -0,0 +1,226 @@
+import assert from "node:assert/strict";
+import { execFileSync } from "node:child_process";
+import { mkdirSync, mkdtempSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { dirname, join, relative } from "node:path";
+import test from "node:test";
+import { fileURLToPath } from "node:url";
+import { patchHashesIn } from "./pi-patch-hash.mjs";
+
+const here = dirname(fileURLToPath(import.meta.url));
+const patchDependencyCheck = join(here, "check-pi-dependencies.mjs");
+const patchCheck = join(here, "check-pi-patches.mjs");
+
+const TARGET = "1.0.1";
+const PATCHED = [
+  {
+    name: "@earendil-works/pi-agent-core",
+    markers: ["hosted_search_update", "localRequestErrorDetails"],
+    extra: "",
+  },
+  {
+    name: "@earendil-works/pi-ai",
+    markers: ["hostedSearch", "withLocalRequestErrors", "AnthropicOAuthTokenError", "Retry-After"],
+    extra: [
+      '+{"openai-completions":{"chat:deepseek-flash":{"baseUrl":"https://api.deepseek.com","compat":{"supportsMidConvoSystemMessages":true}}}}',
+      "diff --git a/dist/index.d.ts b/dist/index.d.ts",
+      "diff --git a/dist/types.d.ts b/dist/types.d.ts",
+      "diff --git a/dist/utils/assistant-message-frame.d.ts b/dist/utils/assistant-message-frame.d.ts",
+      "diff --git a/dist/utils/estimate.d.ts b/dist/utils/estimate.d.ts",
+      "diff --git a/dist/utils/hosted-search.d.ts b/dist/utils/hosted-search.d.ts",
+      "diff --git a/dist/utils/local-request-error.d.ts b/dist/utils/local-request-error.d.ts",
+      "diff --git a/dist/utils/local-request-stream.d.ts b/dist/utils/local-request-stream.d.ts",
+    ].join("\n"),
+  },
+  {
+    name: "@earendil-works/pi-coding-agent",
+    markers: ["hostedSearchReplayProjection", "estimateProjectedContextTokens"],
+    extra: "+export declare function estimateProjectedContextTokens(",
+  },
+];
+const RELEASE_AGE_EXCLUDE = [
+  "chord",
+  "pi-agent-core",
+  "pi-ai",
+  "pi-codemode",
+  "pi-coding-agent",
+  "pi-mcp",
+  "pi-telemetry",
+  "pi-tui",
+].map((name) => `@earendil-works/${name}@${TARGET}`);
+const HASH = `${"0".repeat(63)}1`;
+
+function patchPath(name) {
+  return `patches/${name.replace("@earendil-works/", "@earendil-works__")}@${TARGET}.patch`;
+}
+
+/**
+ * A `.pnpm` entry name as pnpm writes it once it has to shorten the virtual
+ * store directory on a long path: the `patch_hash=` segment is gone even
+ * though the install really is patched. Both checks used to read the hash out
+ * of the resolved symlink, so they called this install unpatched.
+ */
+function storeEntryDir(name, hash, shorten) {
+  const bare = name.replace("@earendil-works/", "");
+  return shorten
+    ? `node_modules/.pnpm/${bare}@${TARGET}_${hash.slice(0, 12)}`
+    : `node_modules/.pnpm/${bare}@${TARGET}_patch_hash=${hash}`;
+}
+
+function run(script, root) {
+  try {
+    const stdout = execFileSync("node", [script, "--root", root], {
+      encoding: "utf8",
+      stdio: ["ignore", "pipe", "pipe"],
+    });
+    return { code: 0, stdout, stderr: "" };
+  } catch (error) {
+    return {
+      code: error.status ?? 1,
+      stdout: error.stdout?.toString() ?? "",
+      stderr: error.stderr?.toString() ?? "",
+    };
+  }
+}
+
+function write(root, path, contents) {
+  const file = join(root, path);
+  mkdirSync(dirname(file), { recursive: true });
+  writeFileSync(file, contents);
+}
+
+function snapshotSection(root, names, hash) {
+  return `lockfileVersion: '9.0'\n\nsnapshots:\n${
+    names.map((name) => `  '${name}@${TARGET}(patch_hash=${hash})': {}`).join("\n")
+  }\n`;
+}
+
+/**
+ * Build a workspace that satisfies both checks: correct pins, every patch
+ * mapped and locked, and the Pi packages installed as patched instances.
+ */
+function workspace({
+  shorten = true,
+  storeNames = PATCHED.map((entry) => entry.name),
+  storeHash = HASH,
+  lockHash = HASH,
+} = {}) {
+  const dir = mkdtempSync(join(tmpdir(), "pi-desktop-patches-"));
+
+  write(
+    dir,
+    "packages/agent-runtime/package.json",
+    JSON.stringify({
+      dependencies: Object.fromEntries([...PATCHED.map((e) => e.name), "@earendil-works/pi-mcp"].map((n) => [n, TARGET])),
+    }),
+  );
+  write(
+    dir,
+    "apps/desktop/package.json",
+    JSON.stringify({
+      devDependencies: { "@earendil-works/pi-ai": TARGET, "@earendil-works/pi-mcp": TARGET },
+    }),
+  );
+  write(dir, "pnpm-lock.yaml", snapshotSection(dir, PATCHED.map((entry) => entry.name), lockHash));
+  write(dir, "node_modules/.pnpm/lock.yaml", snapshotSection(dir, storeNames, storeHash));
+
+  for (const entry of PATCHED) {
+    write(dir, patchPath(entry.name), [entry.markers.join("\n"), entry.extra].filter(Boolean).join("\n"));
+  }
+  // pnpm-workspace.yaml maps each patch, which is what check-pi-patches reads.
+  const workspaceYaml = PATCHED.map(
+    (entry) => `'${entry.name}@${TARGET}': ${patchPath(entry.name)}`,
+  ).join("\n");
+  write(
+    dir,
+    "pnpm-workspace.yaml",
+    `${workspaceYaml}\nminimumReleaseAgeExclude:\n${RELEASE_AGE_EXCLUDE.map((name) => `  - '${name}'`).join("\n")}\n`,
+  );
+
+  const link = (from, to) => {
+    mkdirSync(dirname(from), { recursive: true });
+    symlinkSync(relative(dirname(from), to), from, "dir");
+  };
+  for (const name of PATCHED.map((entry) => entry.name)) {
+    const entryDir = join(dir, storeEntryDir(name, storeHash, shorten), "node_modules", name);
+    write(dir, relative(dir, join(entryDir, "package.json")), JSON.stringify({ name, version: TARGET }));
+    link(join(dir, "packages/agent-runtime/node_modules", name), entryDir);
+  }
+  for (const [scope, name] of [
+    ["apps/desktop", "@earendil-works/pi-ai"],
+    ["apps/desktop", "@earendil-works/pi-mcp"],
+  ]) {
+    write(dir, `${scope}/node_modules/${name}/package.json`, JSON.stringify({ name, version: TARGET }));
+  }
+  return dir;
+}
+
+test("patchHashesIn reads scoped and unscoped snapshot keys, and ignores other versions", () => {
+  const lock = [
+    "  '@scope/pkg@2.0.0(patch_hash=abc123)': {}",
+    "  bare@2.0.0(patch_hash=def456)': {}",
+    "  '@scope/pkg@1.0.0(patch_hash=aaa111)(peer@1)': {}",
+    "  '@scope/pkg@1.0.0(patch_hash=aaa111)(peer@2)': {}",
+    "  '@scope/other@1.0.0(patch_hash=bbb222)': {}",
+  ].join("\n");
+  assert.deepEqual(patchHashesIn(lock, "@scope/pkg", "1.0.0"), ["aaa111"]);
+  assert.deepEqual(patchHashesIn(lock, "bare", "2.0.0"), ["def456"]);
+  assert.deepEqual(patchHashesIn(lock, "@scope/pkg", "9.9.9"), []);
+});
+
+test("patchHashesIn treats the version literally", () => {
+  assert.deepEqual(patchHashesIn("  'pkg@1x0.0(patch_hash=aaa111)': {}", "pkg", "1.0.0"), []);
+});
+
+test("check-pi-dependencies accepts a shortened virtual store entry name", () => {
+  const dir = workspace({ shorten: true });
+  try {
+    const result = run(patchDependencyCheck, dir);
+    assert.equal(result.code, 0, result.stderr);
+  } finally {
+    rmSync(dir, { recursive: true, force: true });
+  }
+});
+
+test("check-pi-patches accepts a shortened virtual store entry name", () => {
+  const dir = workspace({ shorten: true });
+  try {
+    const result = run(patchCheck, dir);
+    assert.equal(result.code, 0, result.stderr);
+  } finally {
+    rmSync(dir, { recursive: true, force: true });
+  }
+});
+
+test("check-pi-dependencies still rejects an install with no patched snapshot", () => {
+  const dir = workspace({ storeNames: [] });
+  try {
+    const result = run(patchDependencyCheck, dir);
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /does not resolve to pnpm's patched package instance/);
+  } finally {
+    rmSync(dir, { recursive: true, force: true });
+  }
+});
+
+test("check-pi-patches rejects an installed patch hash that pnpm-lock.yaml does not record", () => {
+  const dir = workspace({ storeHash: HASH, lockHash: "f".repeat(64) });
+  try {
+    const result = run(patchCheck, dir);
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /absent from pnpm-lock\.yaml/);
+  } finally {
+    rmSync(dir, { recursive: true, force: true });
+  }
+});
+
+test("check-pi-patches rejects a package that is not installed as a patched instance", () => {
+  const dir = workspace({ storeNames: [] });
+  try {
+    const result = run(patchCheck, dir);
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /is not installed as a patched instance/);
+  } finally {
+    rmSync(dir, { recursive: true, force: true });
+  }
+});
\ No newline at end of file