[codex] Harden heartbeat scheduling and runtime controls (#4223)

## Thinking Path

> - Paperclip orchestrates AI agents through issue checkout, heartbeat
runs, routines, and auditable control-plane state
> - The runtime path has to recover from lost local processes, transient
adapter failures, blocked dependencies, and routine coalescing without
stranding work
> - The existing branch carried several reliability fixes across
heartbeat scheduling, issue runtime controls, routine dispatch, and
operator-facing run state
> - These changes belong together because they share backend contracts,
migrations, and runtime status semantics
> - This pull request groups the control-plane/runtime slice so it can
merge independently from board UI polish and adapter sandbox work
> - The benefit is safer heartbeat recovery, clearer runtime controls,
and more predictable recurring execution behavior

## What Changed

- Adds bounded heartbeat retry scheduling, scheduled retry state, and
Codex transient failure recovery handling.
- Tightens heartbeat process recovery, blocker wake behavior, issue
comment wake handling, routine dispatch coalescing, and
activity/dashboard bounds.
- Adds runtime-control MCP tools and Paperclip skill docs for issue
workspace runtime management.
- Adds migrations `0061_lively_thor_girl.sql` and
`0062_routine_run_dispatch_fingerprint.sql`.
- Surfaces retry state in run ledger/agent UI and keeps related shared
types synchronized.

## Verification

- `pnpm exec vitest run
server/src/__tests__/heartbeat-retry-scheduling.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/routines-service.test.ts`
- `pnpm exec vitest run src/tools.test.ts` from `packages/mcp-server`

## Risks

- Medium risk: this touches heartbeat recovery and routine dispatch,
which are central execution paths.
- Migration order matters if split branches land out of order: merge
this PR before branches that assume the new runtime/routine fields.
- Runtime retry behavior should be watched in CI and in local operator
smoke tests because it changes how transient failures are resumed.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5-based coding agent runtime, shell/git tool use
enabled. Exact hosted model build and context window are not exposed in
this Paperclip heartbeat environment.

## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

server/src/__tests__/issues-service.test.ts

@@ -469,6 +469,88 @@ describeEmbeddedPostgres("issueService.list participantAgentId", () => {
     expect(result.map((issue) => issue.id)).toEqual([linkedIssueId]);
   });
 
+  it("filters issues by generic workspace id across execution and project workspace links", async () => {
+    const companyId = randomUUID();
+    const projectId = randomUUID();
+    const projectWorkspaceId = randomUUID();
+    const executionWorkspaceId = randomUUID();
+    const executionLinkedIssueId = randomUUID();
+    const projectLinkedIssueId = randomUUID();
+    const otherIssueId = randomUUID();
+
+    await db.insert(companies).values({
+      id: companyId,
+      name: "Paperclip",
+      issuePrefix: `T${companyId.replace(/-/g, "").slice(0, 6).toUpperCase()}`,
+      requireBoardApprovalForNewAgents: false,
+    });
+
+    await db.insert(projects).values({
+      id: projectId,
+      companyId,
+      name: "Workspace project",
+      status: "in_progress",
+    });
+
+    await db.insert(projectWorkspaces).values({
+      id: projectWorkspaceId,
+      companyId,
+      projectId,
+      name: "Feature workspace",
+      sourceType: "local_path",
+      visibility: "default",
+      isPrimary: false,
+    });
+
+    await db.insert(executionWorkspaces).values({
+      id: executionWorkspaceId,
+      companyId,
+      projectId,
+      projectWorkspaceId,
+      mode: "isolated_workspace",
+      strategyType: "git_worktree",
+      name: "Execution workspace",
+      status: "active",
+      providerType: "git_worktree",
+    });
+
+    await db.insert(issues).values([
+      {
+        id: executionLinkedIssueId,
+        companyId,
+        projectId,
+        projectWorkspaceId,
+        title: "Execution linked issue",
+        status: "done",
+        priority: "medium",
+        executionWorkspaceId,
+      },
+      {
+        id: projectLinkedIssueId,
+        companyId,
+        projectId,
+        projectWorkspaceId,
+        title: "Project linked issue",
+        status: "todo",
+        priority: "medium",
+      },
+      {
+        id: otherIssueId,
+        companyId,
+        projectId,
+        title: "Other issue",
+        status: "todo",
+        priority: "medium",
+      },
+    ]);
+
+    const executionResult = await svc.list(companyId, { workspaceId: executionWorkspaceId });
+    const projectResult = await svc.list(companyId, { workspaceId: projectWorkspaceId });
+
+    expect(executionResult.map((issue) => issue.id)).toEqual([executionLinkedIssueId]);
+    expect(projectResult.map((issue) => issue.id).sort()).toEqual([executionLinkedIssueId, projectLinkedIssueId].sort());
+  });
+
   it("hides archived inbox issues until new external activity arrives", async () => {
     const companyId = randomUUID();
     const userId = "user-1";
@@ -740,6 +822,33 @@ describeEmbeddedPostgres("issueService.list participantAgentId", () => {
     expect(result?.executionState).toBeNull();
     expect(result?.executionWorkspaceSettings).toBeNull();
   });
+
+  it("does not let description preview truncation split multibyte characters", async () => {
+    const companyId = randomUUID();
+    const issueId = randomUUID();
+    const description = `${"x".repeat(1199)}— still valid after truncation`;
+
+    await db.insert(companies).values({
+      id: companyId,
+      name: "Paperclip",
+      issuePrefix: `T${companyId.replace(/-/g, "").slice(0, 6).toUpperCase()}`,
+      requireBoardApprovalForNewAgents: false,
+    });
+
+    await db.insert(issues).values({
+      id: issueId,
+      companyId,
+      title: "Multibyte boundary issue",
+      description,
+      status: "todo",
+      priority: "medium",
+    });
+
+    const [result] = await svc.list(companyId);
+
+    expect(result?.description).toHaveLength(1200);
+    expect(result?.description?.endsWith("—")).toBe(true);
+  });
 });
 
 describeEmbeddedPostgres("issueService.create workspace inheritance", () => {