Address Greptile runtime review concerns

Co-Authored-By: Paperclip <noreply@paperclip.ing>

server/src/__tests__/issue-thread-interactions-service.test.ts

@@ -816,7 +816,7 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
     });
   });
 
-  it("expires request confirmations by default when a user comments after creation", async () => {
+  it("expires request confirmations opted into user-comment supersede after creation", async () => {
     const { companyId, issueId } = await seedConfirmationIssue();
     const commentId = randomUUID();
 
@@ -828,6 +828,7 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
       payload: {
         version: 1,
         prompt: "Proceed with the current draft?",
+        supersedeOnUserComment: true,
       },
     }, {
       userId: "local-board",
@@ -857,7 +858,7 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
     });
   });
 
-  it("keeps request confirmations pending when user-comment supersede is explicitly disabled", async () => {
+  it("keeps request confirmations pending unless user-comment supersede is explicitly enabled", async () => {
     const { companyId, issueId } = await seedConfirmationIssue("Comment supersede opt-out");
 
     await interactionsSvc.create({
@@ -868,7 +869,6 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
       payload: {
         version: 1,
         prompt: "Proceed with the current draft?",
-        supersedeOnUserComment: false,
       },
     }, {
       userId: "local-board",
@@ -902,6 +902,7 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
       payload: {
         version: 1,
         prompt: "Proceed with the current draft?",
+        supersedeOnUserComment: true,
       },
     }, {
       userId: "local-board",
@@ -957,6 +958,7 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
       payload: {
         version: 1,
         prompt: "Proceed with the current draft?",
+        supersedeOnUserComment: true,
       },
     }, {
       userId: "local-board",
@@ -966,6 +968,16 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
       .set({ createdAt, updatedAt: createdAt })
       .where(eq(issueThreadInteractions.id, created.id));
 
+    await db.insert(issueComments).values({
+      id: randomUUID(),
+      companyId,
+      issueId,
+      authorAgentId: randomUUID(),
+      authorType: "agent",
+      body: "Agent-side progress note.",
+      createdAt: new Date("2026-05-18T12:00:30.000Z"),
+      updatedAt: new Date("2026-05-18T12:00:30.000Z"),
+    });
     await db.insert(issueComments).values({
       id: commentId,
       companyId,

server/src/__tests__/plugin-lifecycle-restart.test.ts

@@ -79,6 +79,10 @@ describe("pluginLifecycleManager.restartWorker", () => {
       {} as never,
       { loader: loader as PluginLoader, workerManager },
     );
+    const stopped = vi.fn();
+    const started = vi.fn();
+    lifecycle.on("plugin.worker_stopped", stopped);
+    lifecycle.on("plugin.worker_started", started);
 
     await lifecycle.restartWorker("plugin-1");
 
@@ -87,6 +91,8 @@ describe("pluginLifecycleManager.restartWorker", () => {
     // The bare worker handle should NOT be bounced — the loader handles
     // worker (re)start as part of activate.
     expect(handle.restart).not.toHaveBeenCalled();
+    expect(stopped).not.toHaveBeenCalled();
+    expect(started).not.toHaveBeenCalled();
   });
 
   it("falls back to bouncing the worker handle when the loader has no runtime services", async () => {
@@ -105,11 +111,19 @@ describe("pluginLifecycleManager.restartWorker", () => {
       {} as never,
       { loader: loader as PluginLoader, workerManager },
     );
+    const stopped = vi.fn();
+    const started = vi.fn();
+    lifecycle.on("plugin.worker_stopped", stopped);
+    lifecycle.on("plugin.worker_started", started);
 
     await lifecycle.restartWorker("plugin-1");
 
     expect(loader.unloadSingle).not.toHaveBeenCalled();
     expect(loader.loadSingle).not.toHaveBeenCalled();
     expect(handle.restart).toHaveBeenCalledTimes(1);
+    expect(stopped).toHaveBeenCalledTimes(1);
+    expect(stopped).toHaveBeenCalledWith({ pluginId: "plugin-1", pluginKey: "example.plugin" });
+    expect(started).toHaveBeenCalledTimes(1);
+    expect(started).toHaveBeenCalledWith({ pluginId: "plugin-1", pluginKey: "example.plugin" });
   });
 });

server/src/services/issue-thread-interactions.ts

@@ -1,5 +1,5 @@
 import { isDeepStrictEqual } from "node:util";
-import { and, asc, eq, inArray } from "drizzle-orm";
+import { and, asc, eq, inArray, isNotNull } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
 import {
   documents,
@@ -159,7 +159,7 @@ function shouldReturnAcceptedConfirmationToCreatorAgent(args: {
 }
 
 function shouldSupersedeRequestConfirmationOnUserComment(interaction: RequestConfirmationInteraction) {
-  return interaction.payload.supersedeOnUserComment !== false;
+  return interaction.payload.supersedeOnUserComment === true;
 }
 
 function isCommentAtOrAfterInteraction(args: {
@@ -1059,12 +1059,12 @@ export function issueThreadInteractionService(db: Db) {
           .where(and(
             eq(issueComments.companyId, issue.companyId),
             eq(issueComments.issueId, issue.id),
+            isNotNull(issueComments.authorUserId),
           ))
           .orderBy(asc(issueComments.createdAt)),
       ]);
 
-      const userComments = comments.filter((comment) => comment.authorUserId);
-      if (rows.length === 0 || userComments.length === 0) return [];
+      if (rows.length === 0 || comments.length === 0) return [];
 
       const now = new Date();
       const expired: IssueThreadInteraction[] = [];
@@ -1072,7 +1072,7 @@ export function issueThreadInteractionService(db: Db) {
         const interaction = hydrateInteraction(row) as RequestConfirmationInteraction;
         if (!shouldSupersedeRequestConfirmationOnUserComment(interaction)) continue;
 
-        const supersedingComment = userComments.find((comment) => isCommentAtOrAfterInteraction({
+        const supersedingComment = comments.find((comment) => isCommentAtOrAfterInteraction({
           commentCreatedAt: comment.createdAt,
           interactionCreatedAt: row.createdAt,
         }));

server/src/services/plugin-lifecycle.ts

@@ -810,11 +810,10 @@ export function pluginLifecycleManager(
           "plugin lifecycle: restarting worker (runtime services unavailable; skipping migration re-apply)",
         );
         await handle.restart();
+        emitDomain("plugin.worker_stopped", { pluginId, pluginKey: plugin.pluginKey });
+        emitDomain("plugin.worker_started", { pluginId, pluginKey: plugin.pluginKey });
       }
 
-      emitDomain("plugin.worker_stopped", { pluginId, pluginKey: plugin.pluginKey });
-      emitDomain("plugin.worker_started", { pluginId, pluginKey: plugin.pluginKey });
-
       log.info(
         { pluginId, pluginKey: plugin.pluginKey },
         "plugin lifecycle: plugin reloaded",