refactor(server): extract heartbeat runtime selection (#15746)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Heartbeat execution prepares a runtime, dispatches work, and records
the result.
> - Earlier refactors separated workspace services, scheduling, and
completion.
> - The executor still builds native inputs and records runtime
selection inline.
> - This preparation must preserve admitted inputs and serialize with
Stop.
> - This pull request moves that phase into a typed runtime-selection
module.
> - Reviewers can inspect runtime preparation separately from dispatch
and cleanup.

## Linked Issues or Issue Description

Refs: #15732.

**What existing behavior does this improve?**

Maintainability of heartbeat runtime preparation and selection.

**Subsystem affected**

server/ — orchestration services.

**Current behavior**

The main heartbeat service has 8,128 lines. `executeRun` builds or
restores native inputs, selects sessions and sandbox lifecycle, and
records native or legacy selection inline.

**Proposed behavior**

Move this phase into
`server/src/services/heartbeat/runtime-selection.ts`. The executor calls
`selectHeartbeatRuntime` at the existing boundary and receives an
explicit selection result. The main file becomes 7,275 lines, a
reduction of 853 lines.

**Reason and benefit**

This gives runtime selection its own typed boundary and direct tests. It
preserves existing decisions, database transactions, and cleanup
ordering.

**Breaking changes**

None intended. All public heartbeat exports remain available.

## What Changed

- Move native input assembly, completion contract selection, checkpoint
lookup, runtime persistence, and native workspace-sync preparation into
`selectHeartbeatRuntime`.
- Preserve the row lock and controller lease check that serialize native
selection with cancellation.
- Report lifecycle and ownership changes to the executor immediately,
including when a later preparation step throws.
- Move sandbox lifecycle and model fallback helpers with compatible
public re-exports.
- Add 12 database-backed boundary tests. Update the existing
session-recovery source test and developer guide.

## Verification

- Structural AST comparison against current `master` confirms the
784-line selection block, moved helpers, and remaining service bodies
are unchanged after normalizing boundary callbacks. All 140 public
exports are preserved.
- On final head `2eddaa485f`, all 12 new database-backed tests and 83
existing lifecycle, selection, fallback-warning, and session regression
tests pass (95 total).
- Five executor integration cases passed before the rebase. Their
final-head rerun could not start because the local checkout was removed
during verification; no assertions ran in that last attempt.
- `pnpm -r typecheck` and `pnpm build` both pass on final head.
- Local verification limitations: the full `pnpm test:run` was
attempted, then stopped after database/process startup timeouts in
concurrent local runs. Two unchanged optional real-runner session cases
timed out on the initial run and one isolated retry; they were excluded
from the 95-test focused run. CI also skips those two binary-dependent
cases.
- All CI gates pass on final head `2eddaa485f`: typecheck, build,
general and serialized tests, runner checks, E2E, and canary dry run.
- Greptile reviewed final head at 5/5 with no actionable findings.

## Risks

This boundary controls native admission and cleanup ownership. Losing an
update after a later exception could change resource cleanup. Immediate
callbacks preserve those updates. Tests cover Stop races, lost
controller leases, immutable admitted inputs, competing runtime
selection, and workspace-sync failures. The change adds no schema or API
behavior.

## Model Used

OpenAI Codex, based on GPT-6, with reasoning, code editing, and command
execution. The session does not expose the exact model variant or
context window size.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass (95 focused tests on final
head; broader local limitations documented above)
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

Co-authored-by: Paperclip <noreply@paperclip.ing>

server/src/services/heartbeat/runtime-selection.test.ts

@@ -0,0 +1,229 @@
+import { randomUUID } from "node:crypto";
+import { mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { agents, companies, completionContracts, createDb, EMBEDDED_POSTGRES_TEST_TIMEOUT_MS, heartbeatRuns, issues, nativeRunFinalizations, type Db } from "@paperclipai/db";
+import { eq, sql } from "drizzle-orm";
+import { afterAll, beforeAll, beforeEach, describe, expect, it, vi } from "vitest";
+import { getEmbeddedPostgresTestSupport, startEmbeddedPostgresTestDatabase } from "../../__tests__/helpers/embedded-postgres.js";
+import { CHAT_CONTROL_RECOVERY_ADMISSION_KEY } from "../chat-control-recovery-stop.js";
+import { buildNativeRuntimeContext } from "../native-runtime/runtime-context.js";
+import { nativeRuntimeContextFixture } from "../native-runtime/runtime-context.test-fixture.js";
+import { prepareNativeWorkspaceSync } from "../native-runtime/native-workspace-sync.js";
+import { resolveHeartbeatNativeRuntimeMode } from "../native-runtime/runtime-mode.js";
+import { canonicalNativeRuntimeContextDigest } from "../../vendor/paperclip-runner/index.js";
+import { selectHeartbeatRuntime, type HeartbeatRuntimeSelectionInput } from "./runtime-selection.js";
+
+// Keep the real contract, session, and runtime-selection transactions. Replace only
+// filesystem materialization and sandbox synchronization at their external boundaries.
+vi.mock("../native-runtime/runtime-context.js", async (original) => ({
+  ...await original<typeof import("../native-runtime/runtime-context.js")>(),
+  buildNativeRuntimeContext: vi.fn(async () => nativeRuntimeContextFixture()),
+}));
+vi.mock("../native-runtime/native-workspace-sync.js", async (original) => ({
+  ...await original<typeof import("../native-runtime/native-workspace-sync.js")>(),
+  prepareNativeWorkspaceSync: vi.fn(async () => null),
+}));
+
+const support = await getEmbeddedPostgresTestSupport();
+describe.skipIf(!support.supported)("heartbeat runtime selection boundary", () => {
+  let database: Awaited<ReturnType<typeof startEmbeddedPostgresTestDatabase>>;
+  let db: Db;
+  let instructionRoot: string;
+  beforeAll(async () => {
+    instructionRoot = await mkdtemp(join(tmpdir(), "paperclip-selection-instructions-"));
+    await writeFile(join(instructionRoot, "AGENTS.md"), "Complete the assigned task.\n");
+    database = await startEmbeddedPostgresTestDatabase("paperclip-runtime-selection");
+    db = createDb(database.connectionString);
+    await db.execute(sql`set client_min_messages = warning`);
+  }, EMBEDDED_POSTGRES_TEST_TIMEOUT_MS);
+  afterAll(async () => { await db?.$client.end(); await database?.cleanup(); if (instructionRoot) await rm(instructionRoot, { recursive: true, force: true }); });
+  beforeEach(async () => {
+    await db.execute(sql`truncate table companies restart identity cascade`);
+    vi.clearAllMocks();
+    vi.mocked(prepareNativeWorkspaceSync).mockResolvedValue(null);
+    vi.mocked(buildNativeRuntimeContext).mockImplementation(async () => {
+      const context = nativeRuntimeContextFixture();
+      context.instructions.bundle.rootPath = instructionRoot;
+      return { ...context, aggregateDigest: canonicalNativeRuntimeContextDigest(context) };
+    });
+  });
+
+  async function fixture(adapterType = "paperclip_runner") {
+    const [company] = await db.insert(companies).values({ name: "Runtime selection", issuePrefix: "SEL" }).returning();
+    const [agent] = await db.insert(agents).values({ companyId: company.id, name: "Selecting agent", status: "running", adapterType, adapterConfig: { provider: "codex", model: "gpt-5.6-luna" } }).returning();
+    const [issue] = await db.insert(issues).values({ companyId: company.id, title: "Complete this task", description: "Preserve the requested work", assigneeAgentId: agent.id }).returning();
+    const [run] = await db.insert(heartbeatRuns).values({ companyId: company.id, agentId: agent.id, issueId: issue.id, scopeKind: "issue", status: "running" }).returning();
+    const now = new Date();
+    const input: HeartbeatRuntimeSelectionInput = {
+      run, agent,
+      nativeRuntimeResolution: resolveHeartbeatNativeRuntimeMode({ persisted: run, enabled: true, runtimeConfig: {}, adapterConfig: agent.adapterConfig, agent, issue, target: null, workspaceId: null }),
+      task: { issueRef: issue, issueContext: null, context: { paperclipTaskMarkdown: "Complete this task" }, executionContinuation: null, safeWakeComments: [], safeWakeCommentContext: null, paperclipWakePayload: null, acceptedPlanContinuationWake: false },
+      session: { persistedNativeExecutionInput: null, persistedRunnerProfile: {}, taskSessionCredentialCompatible: true, taskSessionDecodedParams: null, taskSessionForRun: null, isFailedChatRunRetry: false, getFreshSessionHandoff: vi.fn(async () => "Earlier context") },
+      workspace: { persistedExecutionWorkspace: null, executionWorkspace: { cwd: "/tmp/paperclip-runtime-selection", repoUrl: null, repoRef: null, branchName: null }, executionTarget: null, isDotRun: false, projectRepositoryPaths: [],
+        activeEnvironmentLease: { lease: { id: randomUUID(), companyId: company.id, environmentId: null, executionWorkspaceId: null, issueId: issue.id, heartbeatRunId: run.id, status: "active", leasePolicy: "ephemeral", provider: null, providerLeaseId: null, acquiredAt: now, lastUsedAt: now, expiresAt: null, releasedAt: null, failureReason: null, cleanupStatus: null, metadata: null, createdAt: now, updatedAt: now } },
+      },
+      config: { runtimeConfig: {}, runtimeSkillEntries: [], runScopedMentionedSkillKeys: [], instructionCopy: null, agentIdentity: undefined, issueAssigneeOverrides: null, resolvedConfig: {}, managedAiRuntime: undefined },
+      recovery: {}, trace: { providerTraceRequested: false, providerTraceCapture: null },
+      issuesSvc: { addComment: vi.fn() }, runtimeEnv: {}, onAdapterEvent: vi.fn(async () => {}),
+      onNativeLifecycleSelected: vi.fn(), onProviderResourceDisposition: vi.fn(), onNativeOwnershipHeld: vi.fn(), stopControllerLease: vi.fn(),
+    };
+    return { input, issue, run, agent };
+  }
+  const read = (id: string) => db.select().from(heartbeatRuns).where(eq(heartbeatRuns.id, id)).then(rows => rows[0]!);
+  const coordinators = (id: string) => db.select().from(nativeRunFinalizations).where(eq(nativeRunFinalizations.runId, id));
+  const sandbox = { kind: "remote" as const, transport: "sandbox" as const, remoteCwd: "/workspace", reusableLeaseConfigured: false };
+
+  it("persists the native input, completion contract, and coordinator before transferring cleanup ownership", async () => {
+    const { input, run } = await fixture();
+    vi.mocked(prepareNativeWorkspaceSync).mockImplementationOnce(async args => {
+      expect(await read(run.id)).toMatchObject({ runtimeMode: "native", nativeIssueId: input.task.issueRef!.id });
+      expect(await coordinators(run.id)).toHaveLength(1);
+      expect(input.stopControllerLease).toHaveBeenCalledOnce();
+      expect(args).toMatchObject({ runId: run.id, workspaceId: run.id, workspaceLocalDir: input.workspace.executionWorkspace.cwd });
+      return null;
+    });
+    const selected = await selectHeartbeatRuntime(db, input);
+    expect(selected.selected).toBe(true);
+    if (!selected.selected) throw new Error("Expected selection");
+    const saved = await read(run.id);
+    expect(saved).toMatchObject({ runtimeMode: "native", driverKind: "codex_app_server", nativePhase: "observed", nativeSessionId: expect.any(String), runnerInstanceId: selected.nativeRunnerInstanceId,
+      runnerProfileJson: { nativeExecutionInput: selected.nativeExecution, recoveryEventInventoryVersion: 1 } });
+    expect(await db.select().from(completionContracts)).toHaveLength(1);
+    expect(selected.getNativeFreshSessionHandoff).toBe(input.session.getFreshSessionHandoff);
+    expect(input.onNativeOwnershipHeld).not.toHaveBeenCalled();
+  });
+
+  it("persists configured GitHub instruction skills without admitting provider-mentioned skills", async () => {
+    const { input, issue, run } = await fixture();
+    input.config.runScopedMentionedSkillKeys = ["company/test/configured"];
+    input.task.context.paperclipWake = {
+      reason: "External chat message received", externalChatProvider: "github", checkedOutByHarness: true,
+      issue: { id: issue.id, workMode: "standard" },
+      comments: [{ id: "review-comment", body: "Please use /provider-mentioned" }],
+      commentIds: ["review-comment"], latestCommentId: "review-comment",
+      commentWindow: { requestedCount: 1, includedCount: 1, missingCount: 0 }, fallbackFetchNeeded: false,
+    };
+    vi.mocked(buildNativeRuntimeContext).mockImplementationOnce(async () => {
+      const context = nativeRuntimeContextFixture();
+      context.instructions.bundle.rootPath = instructionRoot;
+      context.skills = ["configured", "provider-mentioned"].map(name => ({
+        key: `company/test/${name}`, runtimeName: name, versionId: null,
+        bundle: { ...context.instructions.bundle },
+      }));
+      return { ...context, aggregateDigest: canonicalNativeRuntimeContextDigest(context) };
+    });
+    expect(await selectHeartbeatRuntime(db, input)).toMatchObject({
+      selected: true, nativeExecution: { task: { description: "Configured GitHub instruction skills:\n/configured" } },
+    });
+    expect((await read(run.id)).runnerProfileJson).toMatchObject({
+      nativeExecutionInput: { task: { description: "Configured GitHub instruction skills:\n/configured" } },
+    });
+  });
+
+  it("restores the immutable admitted input and saved checkpoint when newer context arrives", async () => {
+    const { input, run } = await fixture();
+    const selected = await selectHeartbeatRuntime(db, input);
+    if (!selected.selected || !selected.nativeExecution) throw new Error("Expected native selection");
+    const saved = await read(run.id);
+    const profile = { ...saved.runnerProfileJson, sessionCheckpoint: { retained: "checkpoint" } };
+    await db.update(heartbeatRuns).set({ runnerProfileJson: profile }).where(eq(heartbeatRuns.id, run.id));
+    input.run = await read(run.id);
+    input.session.persistedRunnerProfile = profile;
+    input.session.persistedNativeExecutionInput = selected.nativeExecution;
+    input.task.context.paperclipTaskMarkdown = "A newer unrelated request";
+    input.task.safeWakeComments = [{ id: randomUUID(), body: "New direction belongs to a separate wake" }];
+    vi.mocked(buildNativeRuntimeContext).mockClear();
+    const resumed = await selectHeartbeatRuntime(db, input);
+    expect(resumed).toMatchObject({ selected: true, nativeExecution: selected.nativeExecution, nativeRunnerInstanceId: selected.nativeRunnerInstanceId });
+    expect((await read(run.id)).runnerProfileJson).toMatchObject(profile);
+    expect(await db.select().from(completionContracts)).toHaveLength(1);
+    expect(await coordinators(run.id)).toHaveLength(1);
+    expect(buildNativeRuntimeContext).not.toHaveBeenCalled();
+  });
+
+  it("rejects an admitted input bound to another run without replacing the saved runtime", async () => {
+    const { input, run } = await fixture();
+    const selected = await selectHeartbeatRuntime(db, input);
+    if (!selected.selected || !selected.nativeExecution) throw new Error("Expected native selection");
+    const saved = await read(run.id);
+    input.run = saved;
+    input.session.persistedNativeExecutionInput = { ...selected.nativeExecution, binding: { ...selected.nativeExecution.binding, runId: randomUUID() } };
+    await expect(selectHeartbeatRuntime(db, input)).rejects.toThrow("native_execution_input_persisted_binding_mismatch");
+    expect((await read(run.id)).runnerProfileJson).toEqual(saved.runnerProfileJson);
+  });
+
+  it.each(["cancelled", "startup_cancellation"])("does not create a native coordinator when %s wins preparation", async winner => {
+    const { input, run } = await fixture();
+    input.beforeNativeRuntimeSelection = async () => {
+      await db.update(heartbeatRuns).set(winner === "cancelled" ? { status: "cancelled" } : { resultJson: { startupCancellation: { beforeNativeSelection: true } } }).where(eq(heartbeatRuns.id, run.id));
+    };
+    expect(await selectHeartbeatRuntime(db, input)).toEqual({ selected: false });
+    expect(await read(run.id)).toMatchObject({ runtimeMode: "legacy", nativeSessionId: null, completionContractId: null });
+    expect(await coordinators(run.id)).toHaveLength(0);
+    expect(input.stopControllerLease).not.toHaveBeenCalled();
+    expect(prepareNativeWorkspaceSync).not.toHaveBeenCalled();
+  });
+
+  it("reports a lost controller lease before returning without native selection", async () => {
+    const { input, run } = await fixture();
+    await db.update(heartbeatRuns).set({ controllerBootId: randomUUID(), controllerLeaseExpiresAt: new Date(Date.now() + 60_000) }).where(eq(heartbeatRuns.id, run.id));
+    expect(await selectHeartbeatRuntime(db, input)).toEqual({ selected: false });
+    expect(input.onNativeOwnershipHeld).toHaveBeenCalledOnce();
+    expect(input.stopControllerLease).not.toHaveBeenCalled();
+    expect(await coordinators(run.id)).toHaveLength(0);
+  });
+
+  it("rejects a competing persisted legacy selection atomically", async () => {
+    const { input, run } = await fixture();
+    input.beforeNativeRuntimeSelection = async () => {
+      await db.update(heartbeatRuns).set({ runtimeModeResolvedAt: new Date(), runtimeMode: "legacy" }).where(eq(heartbeatRuns.id, run.id));
+    };
+    await expect(selectHeartbeatRuntime(db, input)).rejects.toThrow("native_runtime_mode_conflict");
+    expect((await read(run.id)).runtimeMode).toBe("legacy");
+    expect(await coordinators(run.id)).toHaveLength(0);
+    expect(input.stopControllerLease).not.toHaveBeenCalled();
+  });
+
+  it("reports sandbox teardown policy even when a later preparation step throws", async () => {
+    const { input, run } = await fixture();
+    input.workspace.executionTarget = sandbox;
+    input.beforeNativeRuntimeSelection = async () => { throw new Error("selection interrupted"); };
+    await expect(selectHeartbeatRuntime(db, input)).rejects.toThrow("selection interrupted");
+    expect(input.onNativeLifecycleSelected).toHaveBeenCalledWith({ provider: "codex", harness: "codex_app_server", lifecycleMode: "per_turn", sandboxResource: "destroy_after_turn" });
+    expect(input.onProviderResourceDisposition).toHaveBeenCalledWith("destroy");
+    expect(input.stopControllerLease).not.toHaveBeenCalled();
+    expect(await coordinators(run.id)).toHaveLength(0);
+  });
+
+  it("retains native admission and teardown state if workspace sync preparation fails", async () => {
+    const { input, run } = await fixture();
+    input.workspace.executionTarget = sandbox;
+    vi.mocked(prepareNativeWorkspaceSync).mockRejectedValueOnce(new Error("sync preparation failed"));
+    await expect(selectHeartbeatRuntime(db, input)).rejects.toThrow("sync preparation failed");
+    expect(input.onProviderResourceDisposition).toHaveBeenCalledWith("destroy");
+    expect(input.stopControllerLease).toHaveBeenCalledOnce();
+    expect((await read(run.id)).runtimeMode).toBe("native");
+    expect(await coordinators(run.id)).toHaveLength(1);
+  });
+
+  it("rejects a warm native sandbox that cannot reuse its lease", async () => {
+    const { input, run } = await fixture();
+    input.workspace.executionTarget = { ...sandbox, runnerLifecyclePolicy: { mode: "warm", idleTimeoutMs: 300_000 } };
+    await expect(selectHeartbeatRuntime(db, input)).rejects.toThrow("runner_warm_environment_requires_reusable_lease");
+    expect(input.onNativeLifecycleSelected).not.toHaveBeenCalled();
+    expect(await coordinators(run.id)).toHaveLength(0);
+  });
+
+  it("preserves only server-owned admission and dispatch evidence when recording legacy selection", async () => {
+    const { input, run } = await fixture("process");
+    const admission = { version: 1, kind: "fixture" }, dispatch = { entered: true };
+    await db.update(heartbeatRuns).set({ runnerProfileJson: { [CHAT_CONTROL_RECOVERY_ADMISSION_KEY]: admission, adapterDispatch: dispatch, unrelated: "drop" } }).where(eq(heartbeatRuns.id, run.id));
+    input.trace = { providerTraceRequested: true, providerTraceCapture: { metadata: { id: "trace-id" } } };
+    expect(await selectHeartbeatRuntime(db, input)).toMatchObject({ selected: true, nativeExecution: null, nativeWorkspaceSync: null });
+    expect((await read(run.id)).runnerProfileJson).toEqual({ [CHAT_CONTROL_RECOVERY_ADMISSION_KEY]: admission, adapterDispatch: dispatch, providerTrace: { mode: "raw", traceId: "trace-id", maxBytes: 64 * 1024 * 1024 } });
+    expect(await coordinators(run.id)).toHaveLength(0);
+    expect(input.stopControllerLease).not.toHaveBeenCalled();
+    expect(buildNativeRuntimeContext).not.toHaveBeenCalled();
+  });
+});

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

@@ -461,7 +461,7 @@ describe("capability-gated connection tool refresh", () => {
 
 it("wires exact-session recovery and guarded selected identity into heartbeat persistence", () => {
   const source = readFileSync(
-    new URL("../heartbeat.ts", import.meta.url),
+    new URL("../heartbeat/runtime-selection.ts", import.meta.url),
     "utf8",
   );
   expect(source).toContain("await findNativeSessionResumeRun(db,");