fix: preserve linked PRs and show them in badge tooltips

apps/mobile/src/lib/threadActivityInspector.test.ts

@@ -14,7 +14,7 @@ import {
 import * as DateTime from "effect/DateTime";
 import { describe, expect, it } from "vite-plus/test";
 
-import { buildThreadFeed, type ThreadFeedActivity } from "./threadActivity";
+import type { ThreadFeedActivity } from "./threadActivity";
 import { buildThreadActivityInspector } from "./threadActivityInspector";
 
 const threadId = ThreadId.make("thread-1");
@@ -43,19 +43,15 @@ function itemBase(id: string) {
   };
 }
 
-function activityFor(item: OrchestrationV2TurnItem): ThreadFeedActivity {
+function activityFor(item: OrchestrationV2TurnItem): Pick<ThreadFeedActivity, "projectedItem"> {
   const row: OrchestrationV2ProjectedTurnItem = {
     position: 0,
     visibility: "inherited",
     sourceThreadId,
     sourceItemId: item.id,
     item,
   };
-  const group = buildThreadFeed([row])[0];
-  if (group?.type !== "activity-group" || !group.activities[0]) {
-    throw new Error("Expected an activity group");
-  }
-  return group.activities[0];
+  return { projectedItem: row };
 }
 
 describe("buildThreadActivityInspector", () => {

apps/mobile/src/lib/threadActivityInspector.ts

@@ -72,7 +72,7 @@ function addBlock(
 }
 
 export function buildThreadActivityInspector(
-  activity: ThreadFeedActivity,
+  activity: Pick<ThreadFeedActivity, "projectedItem">,
   support: V2ItemSupport,
   currentThreadId: ThreadId,
 ): ThreadActivityInspectorModel {

apps/server/src/orchestration-v2/Orchestrator.ts

@@ -1,6 +1,7 @@
 import { threadPullRequestsOf } from "@t3tools/shared/threadPullRequests";
 import {
   normalizeThreadPullRequestKey,
+  visibleThreadPullRequests,
   threadPullRequestKeysEqual,
   legacyThreadPullRequestKey,
 } from "@t3tools/shared/threadPullRequests";
@@ -1978,7 +1979,26 @@ const makeOrchestrator = Effect.fn("orchestrationV2.Orchestrator.layer")(functio
                   snapshot: null,
                   stack: null,
                 };
+            const branch = thread.branchPullRequest;
+            const branchKey = branch ? legacyThreadPullRequestKey(branch) : null;
             pullRequests = [
+              ...(command.source === "manual" &&
+              branch &&
+              branchKey &&
+              visibleThreadPullRequests(links).length === 0 &&
+              !threadPullRequestKeysEqual(branchKey, key) &&
+              !links.some((entry) => threadPullRequestKeysEqual(entry, branchKey))
+                ? [
+                    {
+                      ...branchKey,
+                      url: branch.url,
+                      source: "manual" as const,
+                      linkedAt: DateTime.formatIso(now),
+                      snapshot: null,
+                      stack: null,
+                    },
+                  ]
+                : []),
               ...links.filter((entry) => !threadPullRequestKeysEqual(entry, key)),
               link,
             ];

apps/server/src/orchestration-v2/runtimeLayer.test.ts

@@ -1765,6 +1765,102 @@ it.layer(TestLayer)("OrchestrationV2LayerLive lifecycle", (it) => {
     }),
   );
 
+  it.effect("keeps the branch pull request when linking another pull request", () =>
+    Effect.gen(function* () {
+      const orchestrator = yield* OrchestratorV2;
+      const maintenance = yield* ProjectionMaintenanceV2;
+      const projects = yield* ProjectionProjectRepository;
+      const threadId = ThreadId.make("branch-pr-link");
+      const projectId = ProjectId.make("branch-pr-project");
+      yield* projects.upsert({
+        projectId,
+        title: "PR links",
+        workspaceRoot: "/workspace/pr-links",
+        defaultModelSelection: null,
+        defaultThreadEnvMode: null,
+        autoPull: false,
+        scripts: [],
+        createdAt: "2026-09-17T00:00:00.000Z",
+        updatedAt: "2026-09-17T00:00:00.000Z",
+        deletedAt: null,
+      });
+      yield* orchestrator.dispatch({
+        type: "thread.create",
+        createdBy: "user",
+        creationSource: "web",
+        commandId: CommandId.make("branch-pr-create"),
+        threadId,
+        projectId,
+        title: "PR links",
+        modelSelection,
+        runtimeMode: "full-access",
+        interactionMode: "default",
+        branch: "feature/pr-links",
+        worktreePath: null,
+      });
+      const snapshot = yield* orchestrator.getShellSnapshot();
+      yield* orchestrator.dispatch({
+        type: "thread.pull-request.sync",
+        commandId: CommandId.make("branch-pr-discover"),
+        threadId,
+        projectId,
+        snapshotSequence: snapshot.snapshotSequence,
+        expected: {
+          workspaceRoot: "/workspace/pr-links",
+          branch: "feature/pr-links",
+          worktreePath: null,
+          linkedPullRequest: null,
+          branchPullRequest: null,
+        },
+        branchPullRequest: {
+          projectId,
+          repository: "pingdotgg/t3code",
+          number: 1,
+          url: "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/pingdotgg/t3code/pull/1",
+        },
+      });
+      for (const [index, number] of [2, 2, 1, 3].entries()) {
+        yield* orchestrator.dispatch({
+          type: "thread.pull-request.link",
+          commandId: CommandId.make(`branch-pr-link-${index}`),
+          threadId,
+          host: "GitHub.com",
+          repository: "Pingdotgg/T3code",
+          number,
+          url: `https://github.com/pingdotgg/t3code/pull/${number}`,
+          source: "manual",
+        });
+        assert.deepEqual(
+          (yield* orchestrator.getThreadShell(threadId))?.pullRequests?.map((link) => link.number),
+          number === 3 ? [1, 2, 3] : [1, 2],
+        );
+      }
+      yield* orchestrator.dispatch({
+        type: "thread.pull-request.unlink",
+        commandId: CommandId.make("branch-pr-unlink"),
+        threadId,
+        host: "github.com",
+        repository: "pingdotgg/t3code",
+        number: 1,
+      });
+      yield* orchestrator.dispatch({
+        type: "thread.pull-request.link",
+        commandId: CommandId.make("branch-pr-link-after-unlink"),
+        threadId,
+        host: "github.com",
+        repository: "pingdotgg/t3code",
+        number: 4,
+        url: "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/pingdotgg/t3code/pull/4",
+        source: "manual",
+      });
+      assert.isTrue((yield* maintenance.rebuild).valid);
+      assert.deepEqual(
+        (yield* orchestrator.getThreadShell(threadId))?.pullRequests?.map((link) => link.number),
+        [2, 3, 4],
+      );
+    }),
+  );
+
   it.effect("retains multiple pull requests and dismissed stack members through rebuilds", () =>
     Effect.gen(function* () {
       const orchestrator = yield* OrchestratorV2;

apps/server/src/orchestration-v2/testkit/ThreadFork.integration.test.ts

@@ -1160,6 +1160,7 @@ describe("orchestration V2 thread fork", () => {
           },
           {
             type: "checkpoint.rollback",
+            restoreFiles: false,
             commandId: yield* ids.allocate.command({
               fixtureName: "thread-fork-native-prior-turn-source-rollback",
               commandName: "rollback-source-to-alpha",
@@ -1361,6 +1362,7 @@ describe("orchestration V2 thread fork", () => {
           },
           {
             type: "checkpoint.rollback",
+            restoreFiles: false,
             commandId: yield* ids.allocate.command({
               fixtureName: "thread-fork-native-fork-local-rollback",
               commandName: "rollback-fork-to-first",

apps/server/src/orchestration-v2/testkit/fixtures/shared.ts

@@ -760,6 +760,7 @@ export function materializeFixtureInput(input: {
             });
             pushDispatch({
               type: "checkpoint.rollback",
+              restoreFiles: false,
               commandId: yield* idAllocator.allocate.command({
                 fixtureName: input.scenario,
                 commandName: `rollback-${step.checkpointSuffix}`,

apps/server/src/storageCleanup.ts

@@ -16,17 +16,14 @@ import { resolveWorktreeCleanup } from "@t3tools/shared/projectSettings";
 import { makeDrainableWorker } from "@t3tools/shared/DrainableWorker";
 import * as Cause from "effect/Cause";
 import * as Clock from "effect/Clock";
-import * as Context from "effect/Context";
 import * as DateTime from "effect/DateTime";
 import * as Effect from "effect/Effect";
 import * as Equal from "effect/Equal";
 import * as FileSystem from "effect/FileSystem";
-import * as Layer from "effect/Layer";
 import * as Option from "effect/Option";
 import * as Path from "effect/Path";
 import type { PlatformError } from "effect/PlatformError";
 import * as Schedule from "effect/Schedule";
-import type * as Scope from "effect/Scope";
 import * as Stream from "effect/Stream";
 
 import * as ServerConfig from "./config.ts";
@@ -41,14 +38,6 @@ import * as TerminalManager from "./terminal/Manager.ts";
 import * as GitVcsDriver from "./vcs/GitVcsDriver.ts";
 import { withWorkspaceLease } from "./workspace/workspaceLease.ts";
 
-export class StorageCleanup extends Context.Service<
-  StorageCleanup,
-  {
-    readonly start: () => Effect.Effect<void, never, Scope.Scope>;
-    readonly drain: Effect.Effect<void>;
-  }
->()("t3/storageCleanup") {}
-
 const decodeCleanupThread = Schema.decodeUnknownEffect(
   Schema.fromJsonString(OrchestrationV2AppThreadJson),
 );
@@ -508,7 +497,5 @@ export const make = Effect.gen(function* () {
       ),
     );
   });
-  return { start, drain: worker.drain } satisfies StorageCleanup["Service"];
+  return { start, drain: worker.drain };
 });
-
-export const layer = Layer.effect(StorageCleanup, make);

apps/web/src/components/BranchToolbarBranchSelector.tsx

@@ -797,6 +797,7 @@ export function BranchToolbarBranchSelector({
           <ThreadPullRequestBadgeControl
             variant="ghost"
             badge={prBadge}
+            pullRequests={serverThread?.pullRequests ?? []}
             number={prNumber}
             url={prUrl}
             status={displayedPrStatus}

apps/web/src/components/Sidebar.tsx

@@ -1597,6 +1597,7 @@ const SidebarThreadRow = memo(function SidebarThreadRow(props: {
       <ThreadPullRequestBadgeControl
         variant="underline"
         badge={prBadgeShape}
+        pullRequests={thread.pullRequests}
         number={pr?.number ?? currentLinkedPr?.number}
         url={pr?.url ?? currentLinkedPr?.url}
         status={prStatus}

apps/web/src/components/ThreadStatusIndicators.tsx

@@ -204,6 +204,7 @@ export function resolveThreadPullRequestBadgePresentation({
 export function ThreadPullRequestBadgeControl({
   variant,
   badge,
+  pullRequests,
   number,
   url,
   status,
@@ -212,6 +213,7 @@ export function ThreadPullRequestBadgeControl({
 }: {
   variant: "underline" | "ghost";
   badge: ThreadPullRequestBadge | null;
+  pullRequests: ReadonlyArray<ThreadPullRequestLink>;
   number?: number | undefined;
   url?: string | undefined;
   status: PrStatusIndicator | null;
@@ -221,6 +223,7 @@ export function ThreadPullRequestBadgeControl({
   const presentation = resolveThreadPullRequestBadgePresentation({ badge, number, url, status });
   if (presentation === null) return null;
   const isStack = badge?.kind === "stack";
+  const showList = isStack || (badge?.kind === "pull-request" && badge.others > 0);
   const className = cn(
     variant === "ghost"
       ? buttonVariants({ variant: "ghost", size: "xs" })
@@ -266,7 +269,15 @@ export function ThreadPullRequestBadgeControl({
       >
         {content}
       </TooltipTrigger>
-      <TooltipPopup side="top">{presentation.label}</TooltipPopup>
+      <TooltipPopup
+        side="top"
+        variant={showList ? "glass" : "default"}
+        className={
+          showList ? "w-80 max-w-[calc(100vw-2rem)] text-left whitespace-normal" : undefined
+        }
+      >
+        {showList ? <ThreadPullRequestsMiniList pullRequests={pullRequests} /> : presentation.label}
+      </TooltipPopup>
     </Tooltip>
   );
 }

packages/client-runtime/src/handoff.test.ts

@@ -1,6 +1,6 @@
 import { ProviderInstanceId, RunId } from "@t3tools/contracts";
 import { describe, expect, it } from "vite-plus/test";
-import { resolveHandoffEndpoints, type HandoffTimelineRun } from "./handoff";
+import { resolveHandoffEndpoints, type HandoffTimelineRun } from "./handoff.ts";
 
 const from = ProviderInstanceId.make("codex_personal");
 const to = ProviderInstanceId.make("claudeAgent");

packages/client-runtime/src/work-log/presentation.ts

@@ -43,19 +43,6 @@ export function toolItemForDisplay(item: OrchestrationV2TurnItem): Orchestration
   }
 }
 
-/**
- * Activities the worktree setup card already represents. The settled record
- * is rendered by the card on web and mobile, never as a
- * worklog entry, so it is hidden from the activity feed even when it failed.
- */
-export function isWorktreeSetupActivity(kind: string): boolean {
-  return (
-    kind === "setup-script.requested" ||
-    kind === "setup-script.started" ||
-    kind === "worktree-setup"
-  );
-}
-
 export function contextCompactionLabel(
   item: Pick<
     Extract<OrchestrationV2TurnItem, { type: "compaction" }>,