[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

packages/adapter-utils/src/server-utils.test.ts

@@ -221,16 +221,6 @@ describe("runChildProcess", () => {
   });
 });
 
-describe("appendWithByteCap", () => {
-  it("keeps valid UTF-8 when trimming through multibyte text", () => {
-    const output = appendWithByteCap("prefix ", "hello — world", 7);
-
-    expect(output).not.toContain("\uFFFD");
-    expect(Buffer.from(output, "utf8").toString("utf8")).toBe(output);
-    expect(Buffer.byteLength(output, "utf8")).toBeLessThanOrEqual(7);
-  });
-});
-
 describe("renderPaperclipWakePrompt", () => {
   it("keeps the default local-agent prompt action-oriented", () => {
     expect(DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE).toContain("Start actionable work in this heartbeat");
@@ -266,6 +256,42 @@ describe("renderPaperclipWakePrompt", () => {
     expect(prompt).toContain("mark blocked work with the unblock owner/action");
   });
 
+  it("renders dependency-blocked interaction guidance", () => {
+    const prompt = renderPaperclipWakePrompt({
+      reason: "issue_commented",
+      issue: {
+        id: "issue-1",
+        identifier: "PAP-1703",
+        title: "Blocked parent",
+        status: "todo",
+      },
+      dependencyBlockedInteraction: true,
+      unresolvedBlockerIssueIds: ["blocker-1"],
+      unresolvedBlockerSummaries: [
+        {
+          id: "blocker-1",
+          identifier: "PAP-1723",
+          title: "Finish blocker",
+          status: "todo",
+          priority: "medium",
+        },
+      ],
+      commentWindow: {
+        requestedCount: 1,
+        includedCount: 1,
+        missingCount: 0,
+      },
+      commentIds: ["comment-1"],
+      latestCommentId: "comment-1",
+      comments: [{ id: "comment-1", body: "hello" }],
+      fallbackFetchNeeded: false,
+    });
+
+    expect(prompt).toContain("dependency-blocked interaction: yes");
+    expect(prompt).toContain("respond or triage the human comment");
+    expect(prompt).toContain("PAP-1723 Finish blocker (todo)");
+  });
+
   it("includes continuation and child issue summaries in structured wake context", () => {
     const payload = {
       reason: "issue_children_completed",
@@ -335,3 +361,13 @@ describe("renderPaperclipWakePrompt", () => {
     expect(prompt).toContain("Added the helper route and tests.");
   });
 });
+
+describe("appendWithByteCap", () => {
+  it("keeps valid UTF-8 when trimming through multibyte text", () => {
+    const output = appendWithByteCap("prefix ", "hello — world", 7);
+
+    expect(output).not.toContain("\uFFFD");
+    expect(Buffer.from(output, "utf8").toString("utf8")).toBe(output);
+    expect(Buffer.byteLength(output, "utf8")).toBeLessThanOrEqual(7);
+  });
+});