[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>

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

@@ -157,6 +157,35 @@ describe("runChildProcess", () => {
     expect(await waitForPidExit(descendantPid, 2_000)).toBe(true);
   });
 
+  it.skipIf(process.platform === "win32")("cleans up a still-running child after terminal output", async () => {
+    const result = await runChildProcess(
+      randomUUID(),
+      process.execPath,
+      [
+        "-e",
+        [
+          "process.stdout.write(`${JSON.stringify({ type: 'result', result: 'done' })}\\n`);",
+          "setInterval(() => {}, 1000);",
+        ].join(" "),
+      ],
+      {
+        cwd: process.cwd(),
+        env: {},
+        timeoutSec: 0,
+        graceSec: 1,
+        onLog: async () => {},
+        terminalResultCleanup: {
+          graceMs: 100,
+          hasTerminalResult: ({ stdout }) => stdout.includes('"type":"result"'),
+        },
+      },
+    );
+
+    expect(result.timedOut).toBe(false);
+    expect(result.signal).toBe("SIGTERM");
+    expect(result.stdout).toContain('"type":"result"');
+  });
+
   it.skipIf(process.platform === "win32")("does not clean up noisy runs that have no terminal output", async () => {
     const runId = randomUUID();
     let observed = "";

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

@@ -1345,7 +1345,6 @@ export async function runChildProcess(
         let stdout = "";
         let stderr = "";
         let logChain: Promise<void> = Promise.resolve();
-        let childExited = false;
         let terminalResultSeen = false;
         let terminalCleanupStarted = false;
         let terminalCleanupTimer: NodeJS.Timeout | null = null;
@@ -1379,7 +1378,7 @@ export async function runChildProcess(
               onLogError(err, runId, "failed to inspect terminal adapter output");
             }
           }
-          if (!terminalResultSeen || !childExited) return;
+          if (!terminalResultSeen) return;
 
           if (terminalCleanupTimer) return;
           const graceMs = Math.max(0, terminalCleanup.graceMs ?? 5_000);
@@ -1462,7 +1461,6 @@ export async function runChildProcess(
         });
 
         child.on("exit", () => {
-          childExited = true;
           maybeArmTerminalResultCleanup();
         });