fix(runner): repair direct live provider bootstrap

Co-Authored-By: Paperclip <noreply@paperclip.ing>

.github/workflows/runner-protocol-live-evals.yml

@@ -268,11 +268,13 @@ jobs:
             --pack-destination "$RUNNER_TEMP/runner-protocol-build/package"
           package="$(find "$RUNNER_TEMP/runner-protocol-build/package" -maxdepth 1 -type f -name '*.tgz' -print -quit)"
           test -f "$package"
-          npm install --prefix "$RUNNER_TEMP/runner-protocol-build/portable" --omit=dev "$package"
+          pnpm --filter @paperclipai/paperclip-runner deploy --prod \
+            "$RUNNER_TEMP/runner-protocol-build/portable"
           cp "$package" "$RUNNER_TEMP/runner-protocol-build/paperclip-runner.tgz"
           cp packages/paperclip-runner/runner/target/debug/paperclip-runnerd "$RUNNER_TEMP/runner-protocol-build/paperclip-runnerd"
           cp -R packages/paperclip-runner/dist-issue-thread "$RUNNER_TEMP/runner-protocol-build/dist-issue-thread"
-          test -f "$RUNNER_TEMP/runner-protocol-build/portable/node_modules/@paperclipai/paperclip-runner/dist/cli/eval-session.js"
+          test -f "$RUNNER_TEMP/runner-protocol-build/portable/dist/cli/eval-session.js"
+          test -d "$RUNNER_TEMP/runner-protocol-build/portable/node_modules/.pnpm"
           test -x "$RUNNER_TEMP/runner-protocol-build/paperclip-runnerd"
           tar --create --gzip --file runner-protocol-build.tar.gz -C "$RUNNER_TEMP/runner-protocol-build" .
           sha256sum runner-protocol-build.tar.gz > runner-protocol-build.tar.gz.sha256
@@ -433,7 +435,7 @@ jobs:
           python3 .paperclip-evals/evals/paperclip-runner/tools/run_live_roster.py run \
             --roster ".paperclip-evals/evals/paperclip-runner/rosters/$ROSTER_FILE" \
             --case "$CASE_ID" \
-            --runner-cli runner-protocol-build/extracted/portable/node_modules/@paperclipai/paperclip-runner/dist/cli/eval-session.js \
+            --runner-cli runner-protocol-build/extracted/portable/dist/cli/eval-session.js \
             --runner-package runner-protocol-build/extracted/paperclip-runner.tgz \
             --runnerd runner-protocol-build/extracted/paperclip-runnerd \
             --runs-root cell-output/runs \

packages/paperclip-runner/docs/runner-protocol-live-evals.md

@@ -43,6 +43,13 @@ the native daemon, provider dependencies, and the attempt viewer are built
 once and reused by every cell. Because the complete suite requires two matrix
 shards, this workflow accepts a shared concurrency ceiling from 2 through 100.
 
+The reused provider runtime is created with `pnpm deploy --prod` from the
+frozen workspace lock. That preserves the repository's qualified dependency
+versions and patched ACP server bytes. Do not replace this step with a fresh
+`npm install` of the packed Runner tarball: npm cannot apply the workspace's
+`patchedDependencies`, so the resulting ACPX executables no longer match their
+qualified digests.
+
 `all` is intentionally literal. A disabled driver, missing remote profile, or
 unavailable provider is retained as an infrastructure result; it is not
 silently omitted. In particular, the ACPX Pi roster remains visible while Pi
@@ -70,7 +77,9 @@ Claude Managed also requires the four nonsecret
 nonsecret `PAPERCLIP_AWS_AGENTCORE_*` profile variables, including
 `PAPERCLIP_AWS_AGENTCORE_EXECUTION_ROLE_ARN` and the immutable
 `PAPERCLIP_AWS_AGENTCORE_QUALIFICATION_REVISION`; the eval fails closed when
-that deployed revision differs from the pinned roster config. The workflow
+that deployed revision differs from the pinned roster config. The currently
+qualified context-aware harness revision is
+`aws-agentcore-harness-context-v2`. The workflow
 writes the GitHub OIDC token to a mode-`0600` file and never forwards long-lived
 AWS access keys.
 Provision the AgentCore stack with `--github-oidc-provider-arn` so that scoped

packages/paperclip-runner/runner/crates/runner-core/src/aws_agentcore_provider.rs

@@ -2211,7 +2211,7 @@ mod tests {
             context_bucket: "paperclip-context-test".to_owned(),
             context_prefix: "companies/company-test/profiles/profile-test".to_owned(),
             context_kms_key_arn: "arn:aws:kms:us-east-1:123456789012:key/test".to_owned(),
-            qualification_revision: "aws-agentcore-harness-v1".to_owned(),
+            qualification_revision: "aws-agentcore-harness-context-v2".to_owned(),
             event_expiry_days: 90,
             max_estimated_session_cost_usd: 1.0,
             max_iterations: 8,

packages/paperclip-runner/runner/crates/runner-core/src/managed_provider_backend.rs

@@ -43,7 +43,7 @@ const MAX_INSTRUCTIONS_BYTES: usize = 1024 * 1024;
 const QUALIFIED_CLAUDE_MODEL: &str = "claude-sonnet-5";
 const QUALIFIED_CLAUDE_BETA: &str = "managed-agents-2026-04-01";
 const QUALIFIED_AGENTCORE_MODEL: &str = "global.anthropic.claude-sonnet-4-6";
-const QUALIFIED_AGENTCORE_REVISION: &str = "aws-agentcore-harness-v1";
+const QUALIFIED_AGENTCORE_REVISION: &str = "aws-agentcore-harness-context-v2";
 
 fn initial_event_sequence() -> u64 {
     1

packages/paperclip-runner/runner/crates/runner-core/tests/native_provider_backend.rs

@@ -283,7 +283,7 @@ fn managed_prepare_payload(kind: &str) -> Value {
             "contextBucket": "context-bucket",
             "contextPrefix": "companies/company/profiles/profile",
             "contextKmsKeyArn": "arn:aws:kms:us-east-1:123456789012:key/test",
-            "qualificationRevision": "aws-agentcore-harness-v1",
+            "qualificationRevision": "aws-agentcore-harness-context-v2",
             "eventExpiryDays": 90,
             "maxEstimatedSessionCostUsd": 1.0,
             "maxIterations": 8,

packages/paperclip-runner/scripts/runner-protocol-eval-workflow-security.test.mjs

@@ -105,6 +105,15 @@ test("resolves both repositories immutably and bounds total matrix concurrency",
   }
   assert.match(workflow, /matrix_0/u);
   assert.match(workflow, /matrix_1/u);
+  assert.match(
+    workflow,
+    /pnpm --filter @paperclipai\/paperclip-runner deploy --prod/u,
+  );
+  assert.match(
+    workflow,
+    /--runner-cli runner-protocol-build\/extracted\/portable\/dist\/cli\/eval-session\.js/u,
+  );
+  assert.doesNotMatch(workflow, /npm install --prefix/u);
 });
 
 test("publishes only the separately sanitized Evalbook through trusted OIDC code", async () => {

packages/paperclip-runner/src/backends/native-backend-factory.test.ts

@@ -209,7 +209,7 @@ function managedExecution(
         contextBucket: "context-bucket",
         contextPrefix: "companies/company/profiles/profile",
         contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/test",
-        qualificationRevision: "aws-agentcore-harness-v1",
+        qualificationRevision: "aws-agentcore-harness-context-v2",
         eventExpiryDays: 90,
       },
     },
@@ -388,7 +388,7 @@ describe("native backend factory", () => {
     [
       "aws_agentcore" as const,
       "aws_agentcore_harness_api",
-      "aws-agentcore-harness-v1",
+      "aws-agentcore-harness-context-v2",
     ],
   ])("routes %s through runnerd", async (kind, name, version) => {
     const backend = createNativeSessionBackend(managedExecution(kind), {

packages/paperclip-runner/src/contracts/native-execution.test.ts

@@ -235,7 +235,7 @@ describe("NativeExecutionInputV1", () => {
           contextBucket: "paperclip-agentcore-context",
           contextPrefix: "paperclip/runtime",
           contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/test",
-          qualificationRevision: "aws-agentcore-harness-v1",
+          qualificationRevision: "aws-agentcore-harness-context-v2",
           eventExpiryDays: 90,
         },
         maxEstimatedSessionCostUsd: 1,

packages/paperclip-runner/src/live/runnerd-codex-transport.test.ts

@@ -634,6 +634,34 @@ it("derives the ACPX package authority only from the verified dist/cli layout",
   ).toThrow("ACPX sidecar must use the provider package dist/cli layout");
 });
 
+it("keeps a deployed ACPX package inside its pnpm-owned dependency root", async () => {
+  const deployedPackageRoot = await mkdtemp(
+    join(tmpdir(), "paperclip-deployed-provider-package-"),
+  );
+  await mkdir(join(deployedPackageRoot, "dist", "cli"), { recursive: true });
+  await mkdir(join(deployedPackageRoot, "node_modules", ".pnpm"), {
+    recursive: true,
+  });
+  try {
+    expect(
+      runnerdLaunchProfileInternals.acpxProviderPackageAuthority(
+        join(
+          deployedPackageRoot,
+          "dist",
+          "cli",
+          "acpx-runtime-sidecar.cjs",
+        ),
+        deployedPackageRoot,
+      ),
+    ).toEqual({
+      root: deployedPackageRoot,
+      manifest: join(deployedPackageRoot, "package.json"),
+    });
+  } finally {
+    await rm(deployedPackageRoot, { recursive: true, force: true });
+  }
+});
+
 it("requires a provider-pack authority for remote ACPX artifact hashes", () => {
   expect(() =>
     runnerdLaunchProfileInternals.acpxRunnerLaunchProfile(

packages/paperclip-runner/src/live/runnerd-codex-transport.ts

@@ -1549,7 +1549,10 @@ function resolveBuildOwnedCliArtifact(
   );
 }
 
-function acpxProviderPackageAuthority(sidecarScript: string): {
+function acpxProviderPackageAuthority(
+  sidecarScript: string,
+  ownerPackageRoot = packageRoot,
+): {
   root: string;
   manifest: string;
 } {
@@ -1566,10 +1569,19 @@ function acpxProviderPackageAuthority(sidecarScript: string): {
   const sidecarPackageRoot = resolve(cliDirectory, "../..");
   // A local source build consumes pnpm's workspace-owned node_modules tree.
   // A deployed provider pack owns a closed node_modules tree at its own root.
-  return sidecarPackageRoot === packageRoot
+  // Source builds resolve provider dependencies from the monorepo root. A
+  // `pnpm deploy`, however, owns a complete virtual store below the deployed
+  // package root and must not escape to its caller's filesystem. This marker
+  // is generated by pnpm itself and keeps the two layouts unambiguous.
+  const localDependencyRoot = existsSync(
+    resolve(ownerPackageRoot, "node_modules", ".pnpm"),
+  )
+    ? ownerPackageRoot
+    : resolve(ownerPackageRoot, "../..");
+  return sidecarPackageRoot === ownerPackageRoot
     ? {
-        root: resolve(packageRoot, "../.."),
-        manifest: resolve(packageRoot, "package.json"),
+        root: localDependencyRoot,
+        manifest: resolve(ownerPackageRoot, "package.json"),
       }
     : {
         root: sidecarPackageRoot,

server/src/__tests__/managed-agent-profile-routes-authz.test.ts

@@ -123,7 +123,7 @@ describe("managed provider profile route authorization", () => {
           contextBucket: "paperclip-runner-context",
           contextPrefix: "profiles/example",
           contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/example",
-          qualificationRevision: "aws-agentcore-harness-v1",
+          qualificationRevision: "aws-agentcore-harness-context-v2",
           defaultModel: "global.anthropic.claude-sonnet-4-6",
           eventExpiryDays: 90,
         },

server/src/routes/openapi.ts

@@ -4626,7 +4626,7 @@ registry.registerPath({
       configuration: z.record(z.string(), z.unknown()),
       enabled: z.boolean().optional(),
       retentionAcknowledged: z.boolean().optional(),
-      qualification: z.object({ suite: z.literal("aws-agentcore-harness-v1") }).strict().optional(),
+      qualification: z.object({ suite: z.literal("aws-agentcore-harness-context-v2") }).strict().optional(),
     })),
   },
   responses: {

server/src/services/heartbeat-runner-provider-config.test.ts

@@ -87,7 +87,7 @@ describe("Paperclip Runner native provider configuration", () => {
       contextBucket: "paperclip-context",
       contextPrefix: "runner/",
       contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/key-1",
-      qualificationRevision: "aws-agentcore-harness-v1",
+      qualificationRevision: "aws-agentcore-harness-context-v2",
       eventExpiryDays: 90,
     };
     const stored = {
@@ -224,7 +224,7 @@ describe("Paperclip Runner native provider configuration", () => {
           contextBucket: "paperclip-context",
           contextPrefix: "runner/",
           contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/key-1",
-          qualificationRevision: "aws-agentcore-harness-v1",
+          qualificationRevision: "aws-agentcore-harness-context-v2",
           defaultModel: "global.anthropic.claude-sonnet-4-6",
           eventExpiryDays: 90,
           defaultMaxEstimatedSessionCostUsd: 1.25,
@@ -278,7 +278,7 @@ describe("Paperclip Runner native provider configuration", () => {
           contextBucket: "paperclip-context",
           contextPrefix: "runner/",
           contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/key-1",
-          qualificationRevision: "aws-agentcore-harness-v1",
+          qualificationRevision: "aws-agentcore-harness-context-v2",
           defaultModel: "global.anthropic.claude-sonnet-4-6",
           eventExpiryDays: 90,
           defaultMaxEstimatedSessionCostUsd: 1.25,
@@ -352,7 +352,7 @@ describe("Paperclip Runner native provider configuration", () => {
           contextBucket: "paperclip-context",
           contextPrefix: "runner/",
           contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/key-1",
-          qualificationRevision: "aws-agentcore-harness-v1",
+          qualificationRevision: "aws-agentcore-harness-context-v2",
           defaultModel: "global.anthropic.claude-sonnet-4-6",
           eventExpiryDays: 90,
           defaultMaxEstimatedSessionCostUsd: 1.25,

server/src/services/native-runtime/native-session-resume.test.ts

@@ -301,7 +301,7 @@ describe("buildNativeExecutionInput wake projection", () => {
         contextBucket: "paperclip-context",
         contextPrefix: "runner/",
         contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/key-1",
-        qualificationRevision: "aws-agentcore-harness-v1",
+        qualificationRevision: "aws-agentcore-harness-context-v2",
         eventExpiryDays: 90,
       },
       maxEstimatedSessionCostUsd: 1.25,

server/src/services/provider-profile-qualification.ts

@@ -11,7 +11,8 @@ export const CLAUDE_MANAGED_QUALIFICATION = {
 } as const;
 
 export const CLAUDE_MANAGED_QUALIFIED_MODEL = "claude-sonnet-5" as const;
-export const AGENTCORE_QUALIFICATION_SUITE = "aws-agentcore-harness-v1" as const;
+export const AGENTCORE_QUALIFICATION_SUITE =
+  "aws-agentcore-harness-context-v2" as const;
 export const AGENTCORE_QUALIFIED_MODEL = "global.anthropic.claude-sonnet-4-6" as const;
 
 const REVISION_PREFIX = "sha256:";

server/src/services/remote-agent-profiles.test.ts

@@ -28,7 +28,7 @@ const AWS_CONFIGURATION = {
   contextBucket: "paperclip-runner-context",
   contextPrefix: "profiles/example",
   contextKmsKeyArn: "arn:aws:kms:us-east-1:123456789012:key/example",
-  qualificationRevision: "aws-agentcore-harness-v1",
+  qualificationRevision: "aws-agentcore-harness-context-v2",
   defaultModel: "global.anthropic.claude-sonnet-4-6",
   eventExpiryDays: 90,
   defaultMaxEstimatedSessionCostUsd: 1,
@@ -44,7 +44,7 @@ function remoteInput(
     configuration: { ...AWS_CONFIGURATION },
     enabled: false,
     retentionAcknowledged: false,
-    qualification: { suite: "aws-agentcore-harness-v1" },
+    qualification: { suite: "aws-agentcore-harness-context-v2" },
     ...overrides,
   };
 }
@@ -362,7 +362,7 @@ describe("remote agent profile metadata validation", () => {
   });
 
   it("does not allow a qualified AgentCore profile key to be repointed", async () => {
-    const qualification = { suite: "aws-agentcore-harness-v1" };
+    const qualification = { suite: "aws-agentcore-harness-context-v2" };
     const existing = {
       id: "30000000-0000-4000-8000-000000000003",
       companyId: COMPANY_ID,
@@ -506,7 +506,7 @@ describe("remote agent profile metadata validation", () => {
       qualifiedRevision: existingManaged.qualifiedRevision,
     });
 
-    const awsQualification = { suite: "aws-agentcore-harness-v1" };
+    const awsQualification = { suite: "aws-agentcore-harness-context-v2" };
     const existingRemote = {
       id: "30000000-0000-4000-8000-000000000005",
       companyId: COMPANY_ID,
@@ -547,7 +547,7 @@ describe("remote agent profile metadata validation", () => {
   });
 
   it("rejects runtime use when stored identity drifts from the qualified revision", async () => {
-    const qualification = { suite: "aws-agentcore-harness-v1" };
+    const qualification = { suite: "aws-agentcore-harness-context-v2" };
     const qualifiedRevision = computeRemoteAgentProfileRevision({
       service: "aws_bedrock_agentcore_harness",
       configuration: AWS_CONFIGURATION,