[codex] Harden execution reliability and heartbeat tooling (#3679)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - Reliable execution depends on heartbeat routing, issue lifecycle
semantics, telemetry, and a fast enough local verification loop to keep
regressions visible
> - The remaining commits on this branch were mostly server/runtime
correctness fixes plus test and documentation follow-ups in that area
> - Those changes are logically separate from the UI-focused
issue-detail and workspace/navigation branches even when they touch
overlapping issue APIs
> - This pull request groups the execution reliability, heartbeat,
telemetry, and tooling changes into one standalone branch
> - The benefit is a focused review of the control-plane correctness
work, including the follow-up fix that restored the implicit
comment-reopen helpers after branch splitting

## What Changed

- Hardened issue/heartbeat execution behavior, including self-review
stage skipping, deferred mention wakes during active execution, stranded
execution recovery, active-run scoping, assignee resolution, and
blocked-to-todo wake resumption
- Reduced noisy polling/logging overhead by trimming issue run payloads,
compacting persisted run logs, silencing high-volume request logs, and
capping heartbeat-run queries in dashboard/inbox surfaces
- Expanded telemetry and status semantics with adapter/model fields on
task completion plus clearer status guidance in docs/onboarding material
- Updated test infrastructure and verification defaults with faster
route-test module isolation, cheaper default `pnpm test`, e2e isolation
from local state, and repo verification follow-ups
- Included docs/release housekeeping from the branch and added a small
follow-up commit restoring the implicit comment-reopen helpers that were
dropped during branch reconstruction

## Verification

- `pnpm vitest run
server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-telemetry-routes.test.ts`
- `pnpm vitest run server/src/__tests__/http-log-policy.test.ts
server/src/__tests__/heartbeat-run-log.test.ts
server/src/__tests__/health.test.ts`
- `server/src/__tests__/activity-service.test.ts`,
`server/src/__tests__/heartbeat-comment-wake-batching.test.ts`, and
`server/src/__tests__/heartbeat-process-recovery.test.ts` were attempted
on this host but the embedded Postgres harness reported
init-script/data-dir problems and skipped or failed to start, so they
are noted as environment-limited

## Risks

- Medium: this branch changes core issue/heartbeat routing and
reopen/wakeup behavior, so regressions would affect agent execution flow
rather than isolated UI polish
- Because it also updates verification infrastructure, reviewers should
pay attention to whether the new tests are asserting the right failure
modes and not just reshaping harness behavior

## Model Used

- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution enabled

## 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)
- [ ] 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

---------

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

server/src/routes/agents.ts

@@ -964,6 +964,13 @@ export function agentRoutes(db: Db) {
   router.get("/companies/:companyId/agents", async (req, res) => {
     const companyId = req.params.companyId as string;
     assertCompanyAccess(req, companyId);
+    const unsupportedQueryParams = Object.keys(req.query).sort();
+    if (unsupportedQueryParams.length > 0) {
+      res.status(400).json({
+        error: `Unsupported query parameter${unsupportedQueryParams.length === 1 ? "" : "s"}: ${unsupportedQueryParams.join(", ")}`,
+      });
+      return;
+    }
     const result = await svc.list(companyId);
     const canReadConfigs = await actorCanReadConfigurationsForCompany(req, companyId);
     if (canReadConfigs || req.actor.type === "board") {
@@ -1426,7 +1433,7 @@ export function agentRoutes(db: Db) {
     });
     const telemetryClient = getTelemetryClient();
     if (telemetryClient) {
-      trackAgentCreated(telemetryClient, { agentRole: agent.role });
+      trackAgentCreated(telemetryClient, { agentRole: agent.role, agentId: agent.id });
     }
 
     await applyDefaultAgentTaskAssignGrant(
@@ -1514,7 +1521,7 @@ export function agentRoutes(db: Db) {
     });
     const telemetryClient = getTelemetryClient();
     if (telemetryClient) {
-      trackAgentCreated(telemetryClient, { agentRole: agent.role });
+      trackAgentCreated(telemetryClient, { agentRole: agent.role, agentId: agent.id });
     }
 
     await applyDefaultAgentTaskAssignGrant(
@@ -2442,7 +2449,13 @@ export function agentRoutes(db: Db) {
     assertCompanyAccess(req, issue.companyId);
 
     let run = issue.executionRunId ? await heartbeat.getRunIssueSummary(issue.executionRunId) : null;
-    if (run && run.status !== "queued" && run.status !== "running") {
+    if (
+      run &&
+      (
+        (run.status !== "queued" && run.status !== "running") ||
+        run.issueId !== issue.id
+      )
+    ) {
       run = null;
     }