fix(runner): compose native eval instructions

packages/paperclip-runner/src/cli/eval-session-contract.test.ts

@@ -12,6 +12,7 @@ import {
 } from "./eval-session-contract.js";
 import {
   boundedEvalSessionUsage,
+  evalRuntimeSystemInstructions,
   evalSessionProviderVersion,
   prepareEvalRuntimeContext,
 } from "./eval-session.js";
@@ -75,6 +76,11 @@ describe("eval-session request contract", () => {
         join(context.instructions.bundle.rootPath, "AGENTS.md"),
         "utf8",
       )).toContain("Paperclip direct live evaluation");
+      const systemInstructions = evalRuntimeSystemInstructions(context);
+      expect(systemInstructions).toContain("Paperclip direct live evaluation");
+      expect(systemInstructions).toContain(
+        `Read-only instruction sibling root: ${context.instructions.bundle.rootPath}`,
+      );
       expect((await stat(context.instructions.bundle.rootPath)).mode & 0o777)
         .toBe(0o555);
     } finally {

packages/paperclip-runner/src/cli/eval-session.ts

@@ -9,6 +9,7 @@ import {
   PAPERCLIP_EXECUTION_PROMPT,
   PAPERCLIP_EXECUTION_PROMPT_REVISION,
   canonicalNativeRuntimeContextDigest,
+  composeNativeSystemInstructions,
   nativeRuntimePromptDigest,
   parseNativeRuntimeContext,
   type NativeRuntimeContextSnapshot,
@@ -141,6 +142,15 @@ export async function prepareEvalRuntimeContext(
   });
 }
 
+export function evalRuntimeSystemInstructions(
+  runtimeContext: NativeRuntimeContextSnapshot,
+): string {
+  return composeNativeSystemInstructions(
+    runtimeContext,
+    EVAL_RUNTIME_INSTRUCTIONS,
+  );
+}
+
 export function evalSessionProviderVersion(
   request: EvalSessionRequest,
 ): string | null {
@@ -285,6 +295,7 @@ export async function runEvalSessionCli(
       transportOptions: {
         runnerBinary: runnerdPath,
         runtimeContext,
+        baseInstructions: evalRuntimeSystemInstructions(runtimeContext),
         // The transport performs the provider-specific allowlisting. Supplying
         // the source environment here is still required: without it the
         // isolated Codex home has no credential source and runnerd receives no

packages/paperclip-runner/src/live/live-session.test.ts

@@ -662,6 +662,27 @@ describe("Capability live runnerd and Codex session", () => {
     await service.shutdown(session.id);
   });
 
+  it("passes caller-supplied native system instructions to the provider", async () => {
+    const state = providerState();
+    const service = new CapabilityLiveSessionService({
+      transportFactory: fakeTransportFactory(state),
+      transportOptions: {
+        baseInstructions:
+          "Native instructions\n\nRead-only instruction sibling root: /runtime/instructions",
+      },
+    });
+    const session = await service.create();
+
+    expect(
+      state.transports[0]?.requests.find(
+        (request) => request.method === "thread/start",
+      )?.params.baseInstructions,
+    ).toBe(
+      "Native instructions\n\nRead-only instruction sibling root: /runtime/instructions",
+    );
+    await service.shutdown(session.id);
+  });
+
   it("attributes Claude Managed sessions to the pinned immutable Agent version", async () => {
     const state = providerState();
     const managedProfiles: Array<Record<string, unknown> | undefined> = [];

packages/paperclip-runner/src/live/live-session.ts

@@ -2382,7 +2382,8 @@ export class CapabilityLiveSession {
         config: createSkilllessCodexThreadConfig(this.#config.workingDirectory),
         permissions: CODEX_PERMISSION_PROFILE,
         runtimeWorkspaceRoots: [this.#config.workingDirectory],
-        baseInstructions: LIVE_BASE_INSTRUCTIONS,
+        baseInstructions:
+          this.#transportOptions.baseInstructions ?? LIVE_BASE_INSTRUCTIONS,
         persistExtendedHistory: true,
       });
       const resumedThread = record(resumed.thread);
@@ -2407,7 +2408,8 @@ export class CapabilityLiveSession {
         permissions: CODEX_PERMISSION_PROFILE,
         runtimeWorkspaceRoots: [this.#config.workingDirectory],
         approvalPolicy: "never",
-        baseInstructions: LIVE_BASE_INSTRUCTIONS,
+        baseInstructions:
+          this.#transportOptions.baseInstructions ?? LIVE_BASE_INSTRUCTIONS,
         completionContract: LIVE_COMPLETION_CONTRACT,
         dynamicTools: [
           ...tools.map(dynamicToolSpec),

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

@@ -937,6 +937,8 @@ export interface CapabilityRunnerdCodexTransportOptions {
   opencodeProxySha256?: string;
   opencodeRuntimeDirectory?: string;
   environment?: NodeJS.ProcessEnv;
+  /** Provider system instructions supplied by a native execution caller. */
+  baseInstructions?: string;
   closeGraceMs?: number;
   onDiagnostic?: (message: string) => void;
   onEvidence?: (evidence: Readonly<CapabilityRunnerdProcessEvidence>) => void;