[codex] Harden heartbeat runtime cleanup (#4233)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The heartbeat runtime is the control-plane path that turns issue
assignments into agent runs and recovers after process exits.
> - Several edge cases could leave high-volume reads unbounded, stale
runtime services visible, blocked dependency wakes too eager, or
terminal adapter processes still around after output finished.
> - These problems make operator views noisy and make long-running agent
work less predictable.
> - This pull request tightens the runtime/read paths and adds focused
regression coverage.
> - The benefit is safer heartbeat execution and cleaner runtime state
without changing the public task model.

## What Changed

- Bounded high-volume issue/log reads in runtime code paths.
- Hardened heartbeat handling for blocked dependency wakes and terminal
run cleanup.
- Added adapter process cleanup coverage for terminal output cases.
- Added workspace runtime control tests for stale command matching and
stopped services.

## Verification

- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
server/src/__tests__/heartbeat-dependency-scheduling.test.ts
ui/src/components/WorkspaceRuntimeControls.test.tsx`

## Risks

- Medium risk because heartbeat cleanup and runtime filtering affect
active agent execution paths.
- No migrations.

> Checked `ROADMAP.md`; this is runtime hardening and bug-fix work, not
a new roadmap-level feature.

## Model Used

- OpenAI Codex, GPT-5-based coding agent, tool-enabled repository
editing and local test execution.

## 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
- [x] 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

---------

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

ui/src/components/WorkspaceRuntimeControls.test.tsx

@@ -182,6 +182,44 @@ describe("buildWorkspaceRuntimeControlSections", () => {
       }),
     ]);
   });
+
+  it("surfaces running stale runtime services separately from updated commands", () => {
+    const sections = buildWorkspaceRuntimeControlSections({
+      runtimeConfig: {
+        commands: [
+          { id: "web", name: "web", kind: "service", command: "pnpm dev:once --tailscale-auth" },
+        ],
+      },
+      runtimeServices: [
+        createRuntimeService({
+          id: "service-web",
+          serviceName: "web",
+          status: "running",
+          command: "pnpm dev",
+        }),
+      ],
+      canStartServices: true,
+      canRunJobs: true,
+    });
+
+    expect(sections.services).toEqual([
+      expect.objectContaining({
+        title: "web",
+        statusLabel: "stopped",
+        command: "pnpm dev:once --tailscale-auth",
+        runtimeServiceId: null,
+      }),
+    ]);
+    expect(sections.otherServices).toEqual([
+      expect.objectContaining({
+        title: "web",
+        statusLabel: "running",
+        command: "pnpm dev",
+        runtimeServiceId: "service-web",
+        disabledReason: "This runtime service no longer matches a configured workspace command.",
+      }),
+    ]);
+  });
 });
 
 describe("buildWorkspaceRuntimeControlItems", () => {