fix: stop test fixtures from deleting the repository's dependencies

Four fixtures linked the installed dependencies into a throwaway root with a
single directory symlink at <fixture>/node_modules, then ran pnpm inside that
root. pnpm does not recognise the modules directory it finds there and purges
it; with CI=true it does so without a prompt. The purge followed the symlink and
deleted the repository's own node_modules mid-run, so a test suite uninstalled
the workspace it was running in. That is what produced the cascading,
file-unrelated failures a full test:unit run reported, and it happened twice
while running the suites for the adapter re-review.

scripts/lib/fixture-node-modules.ts replaces all four sites: node_modules is a
real directory whose entries are individual symlinks, so a recursive delete
unlinks the fixture's own links instead of walking through one link into the
shared tree. Resolution is unchanged.

tests/unit/fixture-node-modules.test.ts performs the exact recursive delete pnpm
performs and asserts the source tree survives, and check:adapter-inventory now
fails on any reintroduction of the directory-symlink form — verified by putting
the old line back and watching the gate reject it.

A full tests/unit + tests/integration run now leaves the dependencies intact.
removal-fixture, supply-chain and security-followup-archive, the three suites
that had to be excluded before, pass in that run.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

docs/operations/adapter-remediation-ledger.md

@@ -314,8 +314,50 @@ Run on the landed tree. Only what actually passed is claimed as passing.
 | --- | --- | --- |
 | `tests/unit/ci-workflow-generation.test.ts` | 82 failed / 325 passed | Identical on the pre-change baseline (`git stash` comparison). The subprocess gates it spawns cannot run in this sandbox. |
 | `tests/unit/ci-artifact-contract.test.ts` | fails | Unchanged pre-existing sandbox, cgroup and `/tmp` permission behaviour. |
-| `tests/unit/removal-fixture.test.ts`, `tests/unit/supply-chain.test.ts`, `tests/integration/security-followup-archive.test.ts` | destructive | `scripts/lib/removal-fixture.ts:45` and `scripts/check-supply-chain-provider-fixtures.ts:62` symlink the real `node_modules` into a temp fixture root and then run `corepack pnpm` there with `CI=true`. pnpm purges the modules directory it does not recognise, **through the symlink**, deleting the repository's own dependencies mid-run. This is a pre-existing repository hazard, outside the 38 findings, and it is why a full `test:unit` run reports cascading failures. |
+| `tests/unit/security-followup.test.ts`, `tests/unit/provider-guardian-transaction.test.ts` | flaky under full-suite load | Both pass in a fresh process (49 passed). They spawn and reap process groups, so their timing assertions are load sensitive. |
-| `tests/unit/security-followup.test.ts` | flaky under load | Passes in a fresh process; the process-group reaping assertion is timing sensitive. |
+
+### Destructive fixture hazard — fixed
+
+Outside the 38 findings, and found while running the suites for them.
+
+Four sites linked the repository's installed dependencies into a throwaway
+fixture with a single directory symlink at `<fixture>/node_modules`:
+
+- `scripts/lib/removal-fixture.ts`
+- `scripts/check-supply-chain-provider-fixtures.ts`
+- `tests/integration/security-followup-archive.test.ts`
+- `tests/unit/ci-artifact-contract.test.ts`
+
+Each fixture then runs `pnpm` inside itself. pnpm does not recognise the modules
+directory it finds there and purges it; with `CI=true` it does so without a
+prompt. The purge followed the symlink and deleted the **repository's own**
+`node_modules` mid-run — a test suite uninstalling the workspace it was running
+in. That is what produced the cascading, file-unrelated failures a full
+`test:unit` run reported, and it happened twice during this work.
+
+`scripts/lib/fixture-node-modules.ts` replaces all four: `node_modules` is a
+real directory whose entries are individual symlinks, so a recursive delete
+unlinks the fixture's own links instead of walking through one link into the
+shared tree. `tests/unit/fixture-node-modules.test.ts` performs the exact
+recursive delete pnpm performs and asserts the source tree survives, and
+`corepack pnpm check:adapter-inventory` fails on any reintroduction of the
+directory-symlink form.
+
+After the fix a full `tests/unit` + `tests/integration` run leaves the
+dependencies intact and its failures are confined to the two environmental
+files above plus the two flaky-under-load ones:
+
+| File | Failed | Attribution |
+| --- | ---: | --- |
+| `tests/unit/ci-workflow-generation.test.ts` | 82 | Identical on the pre-change baseline (`git stash` comparison). Its subprocess gates cannot run in this sandbox. |
+| `tests/unit/ci-artifact-contract.test.ts` | 19 | Unchanged pre-existing sandbox, cgroup and `/tmp` permission behaviour. |
+| `tests/unit/security-followup.test.ts` | 2 | Passes in isolation. |
+| `tests/unit/provider-guardian-transaction.test.ts` | 1 | Passes in isolation. |
+
+1619 passed / 1723 total, and `tests/unit/removal-fixture.test.ts`,
+`tests/unit/supply-chain.test.ts` and
+`tests/integration/security-followup-archive.test.ts` — the three that had to be
+excluded before — now pass in the full run.
 
 ## Rules for updating this ledger
 

scripts/check-adapter-inventory.ts

@@ -91,6 +91,38 @@ async function main(): Promise<void> {
     }
   }
 
+  // A fixture that links the repository's node_modules with a single directory
+  // symlink is destructive: pnpm running inside that fixture purges the modules
+  // directory it does not recognise, follows the link, and deletes the real
+  // dependencies mid-run. `linkFixtureNodeModules` is the only sanctioned form.
+  const sources = spawnSync(
+    "git",
+    ["grep", "-n", "-e", 'symlink(', "--", "scripts", "tests"],
+    { encoding: "utf8" },
+  );
+  if (sources.status === 0) {
+    for (const line of sources.stdout.split("\n").filter(Boolean)) {
+      if (!line.includes("node_modules")) continue;
+      if (line.startsWith("scripts/lib/fixture-node-modules.ts:")) continue;
+      problems.push(
+        `fixture node_modules: use linkFixtureNodeModules instead — ${line}`,
+      );
+    }
+  }
+  const linkedFixtures = spawnSync(
+    "git",
+    ["grep", "-l", "linkFixtureNodeModules", "--", "scripts", "tests"],
+    { encoding: "utf8" },
+  );
+  if (
+    linkedFixtures.status !== 0 ||
+    linkedFixtures.stdout.split("\n").filter(Boolean).length < 2
+  ) {
+    problems.push(
+      "fixture node_modules: the shared linker has no callers, so it is not the sanctioned path",
+    );
+  }
+
   if (problems.length > 0) {
     for (const problem of problems) console.error(problem);
     process.exitCode = 1;
@@ -100,7 +132,8 @@ async function main(): Promise<void> {
     `Adapter inventory: ${tracked.length} files PASS; ` +
       `service worker asset table: ${
         Object.keys(CACHEABLE_ASSET_CONTENT_TYPES).length
-      } shared extensions PASS`,
+      } shared extensions PASS; ` +
+      `fixture node_modules linking PASS`,
   );
 }
 

scripts/check-supply-chain-provider-fixtures.ts

@@ -12,7 +12,6 @@ import {
   readFile,
   readdir,
   rm,
-  symlink,
   writeFile,
 } from "node:fs/promises";
 import { tmpdir } from "node:os";
@@ -42,6 +41,7 @@ import {
   releaseCandidateManifestSchema,
 } from "./lib/release-candidate.ts";
 import { writeValidatedJsonArtifact } from "./lib/validated-json-artifact.ts";
+import { linkFixtureNodeModules } from "./lib/fixture-node-modules.ts";
 
 const repositoryRoot = process.cwd();
 const fixtureRoot = await mkdtemp(path.join(tmpdir(), "provider-exact-five-fixture-"));
@@ -59,7 +59,7 @@ try {
     recursive: true,
   });
   await rm(path.join(fixtureRoot, "artifacts/release"), { recursive: true, force: true });
-  await symlink(path.join(repositoryRoot, "node_modules"), path.join(fixtureRoot, "node_modules"), "dir");
+  await linkFixtureNodeModules(fixtureRoot, repositoryRoot);
   const git = spawnSync("git", ["show", "-s", "--format=%H%n%ct", "HEAD"], {
     cwd: repositoryRoot,
     encoding: "utf8",

scripts/lib/fixture-node-modules.ts

@@ -0,0 +1,31 @@
+import { lstat, mkdir, readdir, symlink } from "node:fs/promises";
+import path from "node:path";
+
+/**
+ * Links the repository's installed dependencies into a throwaway fixture root.
+ *
+ * The obvious form — one directory symlink at `<fixture>/node_modules` — is
+ * destructive. A fixture runs `pnpm` inside itself, pnpm does not recognise the
+ * modules directory it finds there, and its purge follows the symlink and
+ * deletes the *repository's* real dependencies mid-run. With `CI=true` that
+ * happens without a prompt, so a test suite silently uninstalls the workspace
+ * it is running in.
+ *
+ * `node_modules` is therefore a real directory here, and every entry inside it
+ * is an individual symlink. Package resolution is unchanged, but a recursive
+ * delete unlinks the fixture's own symlinks instead of walking through one link
+ * into the shared tree.
+ */
+export async function linkFixtureNodeModules(
+  fixtureRoot: string,
+  sourceRoot: string = process.cwd(),
+): Promise<void> {
+  const source = path.join(sourceRoot, "node_modules");
+  const target = path.join(fixtureRoot, "node_modules");
+  await mkdir(target, { recursive: true });
+  for (const entry of await readdir(source)) {
+    const from = path.join(source, entry);
+    const stats = await lstat(from);
+    await symlink(from, path.join(target, entry), stats.isDirectory() ? "dir" : "file");
+  }
+}

scripts/lib/removal-fixture.ts

@@ -5,7 +5,6 @@ import {
   readFile,
   readdir,
   rm,
-  symlink,
   writeFile,
 } from "node:fs/promises";
 import path from "node:path";
@@ -14,6 +13,7 @@ import {
   loadCiGateContract,
   parseCiGateContract,
 } from "../contracts/ci-gates.ts";
+import { linkFixtureNodeModules } from "./fixture-node-modules.ts";
 import { generateCiWorkflow } from "../generate-ci-workflow.ts";
 
 export const REMOVAL_FIXTURE_COPY_TARGETS = Object.freeze([
@@ -42,7 +42,7 @@ export async function prepareRemovalFixture(
   for (const target of copyTargets) {
     await cp(target, path.join(root, target), { recursive: true });
   }
-  await symlink(path.resolve("node_modules"), path.join(root, "node_modules"), "dir");
+  await linkFixtureNodeModules(root);
 }
 
 export function runRemovalFixturePnpm(

tests/integration/security-followup-archive.test.ts

@@ -1,5 +1,5 @@
 import { spawnSync } from "node:child_process";
-import { cp, mkdir, mkdtemp, readFile, rm, symlink, writeFile } from "node:fs/promises";
+import { cp, mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import path from "node:path";
 
@@ -15,6 +15,7 @@ import {
   RELEASE_CANDIDATE_MANIFEST_PATH,
   releaseCandidateManifestSchema,
 } from "../../scripts/lib/release-candidate.ts";
+import { linkFixtureNodeModules } from "../../scripts/lib/fixture-node-modules.ts";
 
 it(
   "builds a real candidate assessment and passes the default archived verifier from the captured archive",
@@ -43,7 +44,7 @@ it(
         recursive: true,
         force: true,
       });
-      await symlink(path.join(sourceRoot, "node_modules"), path.join(fixtureRoot, "node_modules"), "dir");
+      await linkFixtureNodeModules(fixtureRoot, sourceRoot);
       const git = spawnSync("git", ["show", "-s", "--format=%H%n%ct", "HEAD"], {
         cwd: sourceRoot,
         encoding: "utf8",

tests/unit/ci-artifact-contract.test.ts

@@ -19,6 +19,7 @@ import {
   validateCiArtifact,
 } from "../../scripts/lib/ci-artifact-validator.ts";
 import { writeCiGateLogAtomic } from "../../scripts/lib/ci-gate-log.ts";
+import { linkFixtureNodeModules } from "../../scripts/lib/fixture-node-modules.ts";
 import { captureCiCandidateArchive, verifyCiCandidateArchive } from "../../scripts/lib/ci-candidate-archive.ts";
 import {
   CANDIDATE_ARCHIVE_USAGE,
@@ -2131,7 +2132,7 @@ async function ensureProviderBaseFixture(): Promise<string> {
     recursive: true,
   });
   await rm(path.join(root, "artifacts/release"), { recursive: true, force: true });
-  await symlink(path.join(sourceRoot, "node_modules"), path.join(root, "node_modules"), "dir");
+  await linkFixtureNodeModules(root, sourceRoot);
   const git = spawnSync("git", ["show", "-s", "--format=%H%n%ct", "HEAD"], {
     cwd: sourceRoot,
     encoding: "utf8",

tests/unit/fixture-node-modules.test.ts

@@ -0,0 +1,89 @@
+import { mkdtemp, mkdir, readdir, readFile, rm, stat, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+
+import { describe, expect, it } from "vitest";
+
+import { linkFixtureNodeModules } from "../../scripts/lib/fixture-node-modules.ts";
+
+/**
+ * A removal or provider fixture runs `pnpm` inside a throwaway copy of the
+ * repository. pnpm does not recognise the modules directory it finds there and
+ * purges it, and with `CI=true` it does so without a prompt. When
+ * `<fixture>/node_modules` was a single directory symlink, that purge followed
+ * the link and deleted the repository's own installed dependencies mid-run —
+ * a test suite uninstalling the workspace it was running in.
+ */
+describe("fixture node_modules linking", () => {
+  async function sourceTree() {
+    const source = await mkdtemp(path.join(tmpdir(), "fixture-source-"));
+    const modules = path.join(source, "node_modules");
+    await mkdir(path.join(modules, "left", "lib"), { recursive: true });
+    await mkdir(path.join(modules, "@scope", "right"), { recursive: true });
+    await mkdir(path.join(modules, ".bin"), { recursive: true });
+    await writeFile(path.join(modules, "left", "lib", "index.js"), "export default 1;\n");
+    await writeFile(path.join(modules, "@scope", "right", "package.json"), "{}\n");
+    await writeFile(path.join(modules, ".modules.yaml"), "{}\n");
+    return source;
+  }
+
+  it("survives a recursive delete of the fixture's node_modules", async () => {
+    const source = await sourceTree();
+    const fixture = await mkdtemp(path.join(tmpdir(), "fixture-root-"));
+    try {
+      await linkFixtureNodeModules(fixture, source);
+
+      // The fixture resolves the same packages...
+      expect(
+        await readFile(
+          path.join(fixture, "node_modules/left/lib/index.js"),
+          "utf8",
+        ),
+      ).toContain("export default 1;");
+      expect(
+        (await readdir(path.join(fixture, "node_modules"))).sort(),
+      ).toEqual([".bin", ".modules.yaml", "@scope", "left"]);
+
+      // ...and this is exactly what pnpm's purge does.
+      await rm(path.join(fixture, "node_modules"), {
+        recursive: true,
+        force: true,
+      });
+
+      // The repository's real dependencies are untouched.
+      expect(
+        await readFile(
+          path.join(source, "node_modules/left/lib/index.js"),
+          "utf8",
+        ),
+      ).toContain("export default 1;");
+      expect(
+        await stat(path.join(source, "node_modules/@scope/right/package.json")),
+      ).toBeDefined();
+      expect(
+        (await readdir(path.join(source, "node_modules"))).sort(),
+      ).toEqual([".bin", ".modules.yaml", "@scope", "left"]);
+    } finally {
+      await rm(source, { recursive: true, force: true });
+      await rm(fixture, { recursive: true, force: true });
+    }
+  });
+
+  it("creates node_modules as a real directory, never a symlink", async () => {
+    const source = await sourceTree();
+    const fixture = await mkdtemp(path.join(tmpdir(), "fixture-root-"));
+    try {
+      await linkFixtureNodeModules(fixture, source);
+      const { lstat } = await import("node:fs/promises");
+      const entry = await lstat(path.join(fixture, "node_modules"));
+      expect(entry.isSymbolicLink()).toBe(false);
+      expect(entry.isDirectory()).toBe(true);
+      expect(
+        (await lstat(path.join(fixture, "node_modules/left"))).isSymbolicLink(),
+      ).toBe(true);
+    } finally {
+      await rm(source, { recursive: true, force: true });
+      await rm(fixture, { recursive: true, force: true });
+    }
+  });
+});