PaperClipAI/server/src/services/native-runtime/runtime-context.test.ts

import { mkdtemp, mkdir, readFile, readdir, chmod, lstat, rm, stat, writeFile } from "node:fs/promises";
import { tmpdir } from "node:os";
import path from "node:path";
import type { Db } from "@paperclipai/db";
import {
  PAPERCLIP_OPERATIONAL_SKILL_KEY,
  type PaperclipSkillEntry,
} from "@paperclipai/adapter-utils/server-utils";
import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";

const serviceMocks = vi.hoisted(() => ({
  exportFiles: vi.fn(),
  readCommittedForRuntime: vi.fn(),
  getEffectiveProfilesForAgent: vi.fn(),
  githubBotConnectionIdsForRun: vi.fn(),
  spekoToolsForSession: vi.fn(),
}));

vi.mock("../voice/speko-agent-tools.js", () => ({ spekoToolsForSession: serviceMocks.spekoToolsForSession }));
vi.mock("../chat-github-tools.js", () => ({
  githubBotConnectionIdsForRun: serviceMocks.githubBotConnectionIdsForRun,
}));

vi.mock("../agent-instructions.js", () => ({
  agentInstructionsService: () => ({ exportFiles: serviceMocks.exportFiles }),
  agentInstructionsBundleMode: (agent: { adapterConfig?: { instructionsBundleMode?: string } }) => agent.adapterConfig?.instructionsBundleMode ?? null,
}));

vi.mock("../agent-instruction-revisions.js", () => ({
  agentInstructionRevisionService: () => ({ readCommittedForRuntime: serviceMocks.readCommittedForRuntime }),
}));

vi.mock("../tool-access.js", () => ({
  toolAccessService: () => ({
    getEffectiveProfilesForAgent: serviceMocks.getEffectiveProfilesForAgent,
  }),
}));

import { createHash } from "node:crypto";
import { context as otelContext, trace } from "@opentelemetry/api";
import { AsyncLocalStorageContextManager } from "@opentelemetry/context-async-hooks";
import { InMemorySpanExporter, SimpleSpanProcessor, TracerProvider } from "@opentelemetry/sdk-trace";
import { withRunExecutionTiming } from "../execution-preparation-timing.js";
import { buildNativeRuntimeContext, resolveNativeRuntimeMcpSnapshot } from "./runtime-context.js";

const temporaryRoots: string[] = [];
let previousPaperclipHome: string | undefined;
let previousInstanceId: string | undefined;

async function makeTreeWritable(target: string): Promise<void> {
  const metadata = await lstat(target).catch(() => null);
  if (!metadata) return;
  if (metadata.isDirectory()) {
    await chmod(target, 0o700);
    for (const entry of await readdir(target)) {
      await makeTreeWritable(path.join(target, entry));
    }
  } else {
    await chmod(target, 0o600);
  }
}

beforeEach(async () => {
  vi.clearAllMocks();
  serviceMocks.readCommittedForRuntime.mockResolvedValue(null);
  serviceMocks.githubBotConnectionIdsForRun.mockResolvedValue(new Set());
  serviceMocks.spekoToolsForSession.mockResolvedValue([]);
  previousPaperclipHome = process.env.PAPERCLIP_HOME;
  previousInstanceId = process.env.PAPERCLIP_INSTANCE_ID;
  const root = await mkdtemp(path.join(tmpdir(), "paperclip-native-context-"));
  temporaryRoots.push(root);
  process.env.PAPERCLIP_HOME = root;
  process.env.PAPERCLIP_INSTANCE_ID = "runtime_context_test";
  serviceMocks.getEffectiveProfilesForAgent.mockResolvedValue({
    agentId: "agent-1",
    profiles: [],
    entries: [{ effect: "include", connectionId: "connection-1" }],
    bindings: [],
    allowedTools: [{ id: "tool-1", connectionId: "connection-1" }],
    allowedToolNames: ["issues.read"],
    installedConnections: [{
      id: "connection-1",
      transport: "mcp_remote",
      enabled: true,
      status: "active",
      healthStatus: "healthy",
    }],
  });
});

afterEach(async () => {
  if (previousPaperclipHome === undefined) delete process.env.PAPERCLIP_HOME;
  else process.env.PAPERCLIP_HOME = previousPaperclipHome;
  if (previousInstanceId === undefined) delete process.env.PAPERCLIP_INSTANCE_ID;
  else process.env.PAPERCLIP_INSTANCE_ID = previousInstanceId;
  // A rejected Promise.all does not cancel the other materializers. Let their
  // bounded local writes settle before removing the read-only asset tree.
  await new Promise((resolve) => setTimeout(resolve, 25));
  while (temporaryRoots.length) {
    const root = temporaryRoots.pop()!;
    await makeTreeWritable(root);
    await rm(root, { recursive: true, force: true });
  }
});

describe("buildNativeRuntimeContext", () => {
  it("uses committed instructions when the disk projection is stale", async () => {
    serviceMocks.exportFiles.mockResolvedValue({
      entryFile: "AGENTS.md",
      files: { "AGENTS.md": "Old disk projection\n", "reference.md": "Sibling reference\n" },
    });
    serviceMocks.readCommittedForRuntime.mockResolvedValue({
      revision: { entryFile: "AGENTS.md" }, content: "Saved canonical instructions\n",
    });
    const context = await buildNativeRuntimeContext({
      db: {} as Db,
      agent: { id: "agent-1", companyId: "company-1", name: "Reviewer", adapterType: "paperclip_runner", adapterConfig: { instructionsBundleMode: "managed" } },
      runId: "run-1", runtimeConfig: {}, runtimeSkillEntries: [],
    });
    expect(await readFile(path.join(context.instructions.bundle.rootPath, context.instructions.entryPath), "utf8"))
      .toBe("Saved canonical instructions\n");
    expect(await readFile(path.join(context.instructions.bundle.rootPath, "reference.md"), "utf8"))
      .toBe("Sibling reference\n");
    expect(serviceMocks.readCommittedForRuntime).toHaveBeenCalledWith({ companyId: "company-1", agentId: "agent-1" });
  });

  it("does not substitute canonical managed instructions into an external bundle", async () => {
    serviceMocks.exportFiles.mockResolvedValue({ entryFile: "AGENTS.md", files: { "AGENTS.md": "External instructions\n" } });
    const context = await buildNativeRuntimeContext({
      db: {} as Db,
      agent: { id: "agent-1", companyId: "company-1", name: "Reviewer", adapterConfig: { instructionsBundleMode: "external" } },
      runId: "run-1", runtimeConfig: {}, runtimeSkillEntries: [],
    });
    expect(await readFile(path.join(context.instructions.bundle.rootPath, context.instructions.entryPath), "utf8"))
      .toBe("External instructions\n");
    expect(serviceMocks.readCommittedForRuntime).not.toHaveBeenCalled();
  });

  it("keeps the pinned prompt immutable while exposing the registered editable instruction copy", async () => {
    serviceMocks.exportFiles.mockResolvedValue({
      entryFile: "instructions/CHARter.md",
      files: { "instructions/CHARter.md": "Original instructions.\n" },
    });
    const workingRoot = path.join(temporaryRoots.at(-1)!, "private-run-copy");
    await mkdir(path.join(workingRoot, "instructions"), { recursive: true });
    await writeFile(path.join(workingRoot, "instructions/CHARter.md"), "Original instructions.\n");
    const context = await buildNativeRuntimeContext({
      db: {} as Db,
      agent: { id: "agent-1", companyId: "company-1", name: "Reviewer", adapterType: "paperclip_runner", adapterConfig: {} },
      runId: "run-1",
      runtimeConfig: {},
      runtimeSkillEntries: [],
      instructionWorkingCopy: { rootPath: workingRoot, entryPath: "instructions/CHARter.md" },
    });
    expect(context.instructions.workingCopy).toEqual({ rootPath: workingRoot, entryPath: "instructions/CHARter.md" });
    await writeFile(path.join(workingRoot, "instructions/CHARter.md"), "Persist this next time.\n");
    expect(await readFile(path.join(context.instructions.bundle.rootPath, context.instructions.entryPath), "utf8"))
      .toBe("Original instructions.\n");
  });

  it.each(["disabled", "degraded"] as const)(
    "omits an unavailable native MCP connection when it is %s without aborting runtime context creation",
    async (unavailableState) => {
      serviceMocks.exportFiles.mockResolvedValue({
        entryFile: "AGENTS.md",
        files: { "AGENTS.md": "Continue work without unavailable apps.\n" },
      });
      serviceMocks.getEffectiveProfilesForAgent.mockResolvedValue({
        agentId: "agent-1",
        profiles: [],
        entries: [{ effect: "include", connectionId: "connection-1" }],
        bindings: [],
        allowedTools: [{ id: "tool-1", connectionId: "connection-1" }],
        allowedToolNames: ["issues.read"],
        installedConnections: [{
          id: "connection-1",
          transport: "mcp_remote",
          enabled: unavailableState !== "disabled",
          status: unavailableState === "disabled" ? "disabled" : "active",
          healthStatus: unavailableState === "degraded" ? "degraded" : "healthy",
        }],
      });

      const context = await buildNativeRuntimeContext({
        db: {} as Db,
        agent: {
          id: "agent-1",
          companyId: "company-1",
          name: "Reviewer",
          adapterType: "paperclip_runner",
          adapterConfig: {},
        },
        runId: "run-1",
        runtimeConfig: {},
        runtimeSkillEntries: [],
      });

      expect(context.mcp.bindingId).toBeNull();
      expect(context.mcp.assignmentSetId).toMatch(/^sha256:[a-f0-9]{64}$/);
    },
  );

  it("keeps healthy native MCP connections when another assigned connection is unavailable", async () => {
    serviceMocks.exportFiles.mockResolvedValue({
      entryFile: "AGENTS.md",
      files: { "AGENTS.md": "Continue work with the apps that are available.\n" },
    });
    serviceMocks.getEffectiveProfilesForAgent.mockResolvedValue({
      agentId: "agent-1",
      profiles: [],
      entries: [
        { effect: "include", connectionId: "connection-expired" },
        { effect: "include", connectionId: "connection-healthy" },
      ],
      bindings: [],
      allowedTools: [
        { id: "tool-expired", connectionId: "connection-expired" },
        { id: "tool-healthy", connectionId: "connection-healthy" },
      ],
      allowedToolNames: ["expired.read", "healthy.read"],
      installedConnections: [
        {
          id: "connection-expired",
          transport: "mcp_remote",
          enabled: true,
          status: "active",
          healthStatus: "degraded",
        },
        {
          id: "connection-healthy",
          transport: "mcp_remote",
          enabled: true,
          status: "active",
          healthStatus: "healthy",
        },
      ],
    });

    const context = await buildNativeRuntimeContext({
      db: {} as Db,
      agent: {
        id: "agent-1",
        companyId: "company-1",
        name: "Reviewer",
        adapterType: "paperclip_runner",
        adapterConfig: {},
      },
      runId: "run-1",
      runtimeConfig: {},
      runtimeSkillEntries: [],
    });

    expect(context.mcp.bindingId).toBe("native-mcp:run-1");
    expect(context.mcp.assignmentSetId).toMatch(/^sha256:[a-f0-9]{64}$/);
  });

  it("materializes every instruction and selected-skill file as immutable, content-addressed context", async () => {
    serviceMocks.exportFiles.mockResolvedValue({
      entryFile: "AGENTS.md",
      files: {
        "AGENTS.md": "Follow the agent instructions.\n",
        "references/policy.md": "Company policy sibling.\n",
      },
    });
    const sourceRoot = await mkdtemp(path.join(tmpdir(), "paperclip-native-skill-"));
    temporaryRoots.push(sourceRoot);
    const selectedRoot = path.join(sourceRoot, "reviewer");
    const unselectedRoot = path.join(sourceRoot, "unused");
    await mkdir(path.join(selectedRoot, "references"), { recursive: true });
    await mkdir(unselectedRoot, { recursive: true });
    await writeFile(path.join(selectedRoot, "SKILL.md"), "# Reviewer\nUse the checklist.\n");
    await writeFile(path.join(selectedRoot, "references", "checklist.md"), "- Verify tests\n");
    await writeFile(path.join(unselectedRoot, "SKILL.md"), "# Not selected\n");
    const entries: PaperclipSkillEntry[] = [
      { key: "company-1/reviewer", runtimeName: "reviewer", source: selectedRoot, versionId: "version-1" },
      { key: "company-1/unused", runtimeName: "unused", source: unselectedRoot, versionId: "version-2" },
    ];
    const input = {
      db: {} as Db,
      agent: {
        id: "agent-1",
        companyId: "company-1",
        name: "Reviewer",
        adapterType: "paperclip_runner",
        adapterConfig: {},
      },
      runId: "run-1",
      runtimeConfig: { paperclipSkillSync: { desiredSkills: ["company-1/reviewer"] } },
      runtimeSkillEntries: entries,
    };

    const context = await buildNativeRuntimeContext(input);
    const repeated = await buildNativeRuntimeContext(input);

    expect(serviceMocks.exportFiles).toHaveBeenCalledWith(input.agent, { rejectSymlinks: true });
    expect(serviceMocks.getEffectiveProfilesForAgent).toHaveBeenCalledWith("company-1", "agent-1");
    expect(context.instructions.entryPath).toBe("AGENTS.md");
    expect(await readFile(path.join(context.instructions.bundle.rootPath, "AGENTS.md"), "utf8"))
      .toBe("Follow the agent instructions.\n");
    expect(await readFile(path.join(context.instructions.bundle.rootPath, "references", "policy.md"), "utf8"))
      .toBe("Company policy sibling.\n");
    const unselected = await buildNativeRuntimeContext({ ...input, runtimeConfig: {} });
    expect(unselected.skills).toEqual([]);
    expect(context.skills).toHaveLength(1);
    expect(context.skills[0]).toMatchObject({
      key: "company-1/reviewer",
      runtimeName: "reviewer",
      versionId: "version-1",
    });
    expect(await readFile(path.join(context.skills[0]!.bundle.rootPath, "SKILL.md"), "utf8"))
      .toContain("Use the checklist");
    expect(await readFile(path.join(context.skills[0]!.bundle.rootPath, "references", "checklist.md"), "utf8"))
      .toBe("- Verify tests\n");
    expect((await stat(context.instructions.bundle.rootPath)).mode & 0o222).toBe(0);
    expect((await stat(path.join(context.instructions.bundle.rootPath, "AGENTS.md"))).mode & 0o222).toBe(0);
    expect((await stat(context.skills[0]!.bundle.rootPath)).mode & 0o222).toBe(0);
    expect(context.mcp).toMatchObject({
      bindingId: "native-mcp:run-1",
      assignmentSetId: expect.stringMatching(/^sha256:[a-f0-9]{64}$/),
      digest: expect.stringMatching(/^[a-f0-9]{64}$/),
    });
    expect(repeated.aggregateDigest).toBe(context.aggregateDigest);
    expect(repeated.instructions.bundle.rootPath).toBe(context.instructions.bundle.rootPath);
    expect(repeated.skills[0]!.bundle.rootPath).toBe(context.skills[0]!.bundle.rootPath);
  });

  it("does not materialize assigned skills or external MCP in preconfigured mode", async () => {
    serviceMocks.exportFiles.mockResolvedValue({ entryFile: "AGENTS.md", files: { "AGENTS.md": "Test\n" } });
    const context = await buildNativeRuntimeContext({ db: {} as Db,
      agent: { id: "agent-1", companyId: "company-1", name: "Reviewer", adapterType: "paperclip_runner", adapterConfig: {} },
      runId: "run-1", runtimeConfig: { homeMode: "preconfigured", paperclipSkillSync: { desiredSkills: ["missing"] } },
      runtimeSkillEntries: [{ key: "missing", runtimeName: "missing", source: "/does/not/exist", sourceStatus: "missing" }],
    });
    expect(context.skills).toEqual([]);
    expect(context.mcp.bindingId).toBeNull();
    expect(serviceMocks.getEffectiveProfilesForAgent).not.toHaveBeenCalled();
  });

  it("fails closed for a missing assigned skill and omits a stale legacy operational skill", async () => {
    serviceMocks.exportFiles.mockResolvedValue({ entryFile: "AGENTS.md", files: { "AGENTS.md": "Test\n" } });
    const base = {
      db: {} as Db,
      agent: {
        id: "agent-1",
        companyId: "company-1",
        name: "Reviewer",
        adapterType: "paperclip_runner",
        adapterConfig: {},
      },
      runId: "run-1",
    };
    await expect(buildNativeRuntimeContext({
      ...base,
      runtimeConfig: { paperclipSkillSync: { desiredSkills: ["company-1/missing"] } },
      runtimeSkillEntries: [{
        key: "company-1/missing",
        runtimeName: "missing",
        source: "/does/not/exist",
        sourceStatus: "missing",
        missingDetail: "assigned skill checkout is unavailable",
      }],
    })).rejects.toThrow("assigned skill checkout is unavailable");
    const supportedRoot = await mkdtemp(path.join(tmpdir(), "paperclip-native-supported-skill-"));
    temporaryRoots.push(supportedRoot);
    await writeFile(path.join(supportedRoot, "SKILL.md"), "# Supported\n");
    const context = await buildNativeRuntimeContext({
      ...base,
      runtimeConfig: {
        paperclipSkillSync: {
          desiredSkills: [PAPERCLIP_OPERATIONAL_SKILL_KEY, "company-1/supported"],
        },
      },
      runtimeSkillEntries: [
        {
          key: PAPERCLIP_OPERATIONAL_SKILL_KEY,
          runtimeName: "paperclip",
          source: "/unused",
        },
        {
          key: "company-1/supported",
          runtimeName: "supported",
          source: supportedRoot,
        },
      ],
    });
    expect(context.skills.map((skill) => skill.key)).toEqual(["company-1/supported"]);
  });
});


it("pins both permitted GitHub tool catalogs even when another user’s health probe reports missing credentials", async () => {
  const connections = ["github-A", "github-B"].map((id) => ({
    id, status: "active", enabled: true, healthStatus: "missing_secret", transport: "mcp_remote",
    config: { sourceTemplateKey: "github" }, transportConfig: {},
  }));
  serviceMocks.getEffectiveProfilesForAgent.mockResolvedValue({
    entries: connections.map((connection) => ({ effect: "include", connectionId: connection.id })),
    installedConnections: connections,
    allowedTools: connections.map((connection) => ({ id: `${connection.id}-get_me`, connectionId: connection.id })),
  });
  const limit = vi.fn(async () => [{ responsibleUserId: "A", activeIdentityContextId: "context-A" }]);
  const db = { select: () => ({ from: () => ({ where: () => ({ limit }) }) }) } as unknown as Db;
  const snapshot = await resolveNativeRuntimeMcpSnapshot({ db, agent: { id: "agent-1", companyId: "company-1" }, runId: "run-1" });
  const expected = createHash("sha256").update(JSON.stringify({
    version: 1, agentId: "agent-1", connections: ["github-A", "github-B"],
    tools: ["github-A-get_me", "github-B-get_me"],
  })).digest("hex");
  expect(snapshot.digest).toBe(expected);
  expect(snapshot.bindingId).toBe("native-mcp:run-1");
  expect(limit).toHaveBeenCalledOnce();
});

it("pins channel tools only when the current task run is bound to that bot", async () => {
  serviceMocks.getEffectiveProfilesForAgent.mockResolvedValue({
    entries: [{ effect: "include", connectionId: "bot-connection" }],
    installedConnections: [{
      id: "bot-connection", status: "active", enabled: true, healthStatus: "healthy",
      transport: "chat_sdk", config: { sourceTemplateKey: "github-chat" }, transportConfig: {},
    }],
    allowedTools: [{ id: "bot-read-pr", connectionId: "bot-connection" }],
  });
  const input = { db: {} as Db, agent: { id: "agent-1", companyId: "company-1" }, runId: "run-1" };
  expect((await resolveNativeRuntimeMcpSnapshot(input)).bindingId).toBeNull();
  serviceMocks.githubBotConnectionIdsForRun.mockResolvedValue(new Set(["bot-connection"]));
  expect((await resolveNativeRuntimeMcpSnapshot(input)).bindingId).toBe("native-mcp:run-1");
  expect(serviceMocks.githubBotConnectionIdsForRun).toHaveBeenLastCalledWith(input.db, "company-1", "agent-1", "run-1");
});

it("pins a voice tool only when the current requester can call through that assigned endpoint", async () => {
  serviceMocks.getEffectiveProfilesForAgent.mockResolvedValue({ entries: [{ effect: "include", connectionId: "voice-connection" }], installedConnections: [{ id: "voice-connection", status: "active", enabled: true, healthStatus: "healthy", transport: "voice", config: { provider: "speko" }, transportConfig: {} }], allowedTools: [{ id: "phone-tool", connectionId: "voice-connection" }] });
  const limit = vi.fn().mockResolvedValue([{ contextSnapshot: { issueId: "task-1" }, activeIdentityContextId: "identity-1" }]);
  const db = { select: () => ({ from: () => ({ where: () => ({ limit }) }) }) } as unknown as Db;
  const input = { db, agent: { id: "agent-1", companyId: "company-1" }, runId: "run-1" };
  expect((await resolveNativeRuntimeMcpSnapshot(input)).bindingId).toBeNull();
  serviceMocks.spekoToolsForSession.mockResolvedValue([{ connectionId: "voice-connection" }]);
  expect((await resolveNativeRuntimeMcpSnapshot(input)).bindingId).toBe("native-mcp:run-1");
  expect(serviceMocks.spekoToolsForSession).toHaveBeenLastCalledWith(db, { companyId: "company-1", agentId: "agent-1", runId: "run-1", issueId: "task-1", identityContextId: "identity-1" });
});

it("keeps instructions, selected skills, and MCP concurrent and distinguishes cold materialization from warm verification", async () => {
  vi.stubEnv("OTEL_EXPORTER_OTLP_ENDPOINT", "http://collector.test");
  const exporter = new InMemorySpanExporter();
  const provider = new TracerProvider({ spanProcessors: [new SimpleSpanProcessor({ exporter })] });
  const manager = new AsyncLocalStorageContextManager().enable();
  expect(otelContext.setGlobalContextManager(manager)).toBe(true);
  expect(trace.setGlobalTracerProvider(provider)).toBe(true);
  let release!: () => void;
  const gate = new Promise<void>(resolve => { release = resolve; });
  serviceMocks.exportFiles.mockImplementation(async () => {
    await gate;
    return { entryFile: "AGENTS.md", files: { "AGENTS.md": "Private fixture instructions" } };
  });
  const source = path.join(temporaryRoots.at(-1)!, "selected-skill");
  await mkdir(source);
  await writeFile(path.join(source, "SKILL.md"), "Private skill fixture");
  const input = {
    db: {} as Db, agent: { id: "agent-1", companyId: "company-1", name: "Reviewer", adapterConfig: {} },
    runId: "concurrent-context", runtimeConfig: { paperclipSkillSync: { desiredSkills: ["selected"] } },
    runtimeSkillEntries: [{ key: "selected", runtimeName: "selected", source }],
  };
  const pending = withRunExecutionTiming(input.runId, () => buildNativeRuntimeContext(input));
  try {
    await vi.waitFor(() => {
      expect(exporter.getFinishedSpans().map(span => span.name)).toEqual(expect.arrayContaining(["runtime_context.skills", "runtime_context.mcp"]));
    });
    expect(exporter.getFinishedSpans().some(span => span.name === "runtime_context.instructions")).toBe(false);
    release();
    const cold = await pending;
    expect(cold.skills).toHaveLength(1);
    expect(exporter.getFinishedSpans().some(span => span.name === "runtime_context.asset_materialize")).toBe(true);
    exporter.reset();
    const warm = await withRunExecutionTiming(input.runId, () => buildNativeRuntimeContext(input));
    expect(warm.aggregateDigest).toBe(cold.aggregateDigest);
    const spans = exporter.getFinishedSpans();
    expect(spans.some(span => span.name === "runtime_context.asset_verify")).toBe(true);
    expect(spans.some(span => span.name === "runtime_context.asset_materialize")).toBe(false);
    expect(JSON.stringify(spans.map(span => span.attributes))).not.toContain("Private");
    const siblings = spans.filter(span => ["runtime_context.instructions", "runtime_context.skills", "runtime_context.mcp"].includes(span.name));
    expect(siblings).toHaveLength(3);
    expect(new Set(siblings.map(span => span.parentSpanContext?.spanId)).size).toBe(1);
  } finally {
    release();
    await pending.catch(() => undefined);
    trace.disable(); otelContext.disable(); manager.disable();
    await provider.shutdown();
    vi.unstubAllEnvs();
  }
});