diff --git a/apps/server/src/git/isolatedRunWorkspaceFile.ts b/apps/server/src/git/isolatedRunWorkspaceFile.ts
index 807fb13d0b9a..3a82a6c28e1c 100644
--- a/apps/server/src/git/isolatedRunWorkspaceFile.ts
+++ b/apps/server/src/git/isolatedRunWorkspaceFile.ts
@@ -9,6 +9,7 @@
  *
  * @module isolatedRunWorkspaceFile
  */
+import { writeFileStringAtomically } from "@t3tools/shared/atomicWrite";
 import { fromJsonStringPretty, fromLenientJson } from "@t3tools/shared/schemaJson";
 import * as Effect from "effect/Effect";
 import * as FileSystem from "effect/FileSystem";
@@ -62,7 +63,8 @@ export const writeIsolatedRunWorkspaceFile = Effect.fn("writeIsolatedRunWorkspac
     );
     const target = WorkspaceRepositories.isolatedRunWorkspaceFilePath(input.container);
     const contents = yield* encodeDocument({ ...document, folders });
-    yield* fileSystem.writeFileString(target, `${contents}\n`);
+    // Atomic, so a file that exists is a complete one and callers can skip it.
+    yield* writeFileStringAtomically({ filePath: target, contents: `${contents}\n` });
     return target;
   },
 );
diff --git a/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.test.ts b/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.test.ts
index 3e6e3b906ef3..045f04ca9f72 100644
--- a/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.test.ts
+++ b/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.test.ts
@@ -14,7 +14,10 @@ import * as GitVcsDriver from "../../vcs/GitVcsDriver.ts";
 import * as VcsProcess from "../../vcs/VcsProcess.ts";
 import * as WorkspaceRepositories from "../../workspace/WorkspaceRepositories.ts";
 import * as ThreadManagement from "../ThreadManagementService.ts";
-import { repairMultiRepoForkWorktrees } from "./repairMultiRepoForkWorktrees.ts";
+import {
+  repairMultiRepoForkWorktrees,
+  writeMultiRepoForkWorkspaceFiles,
+} from "./repairMultiRepoForkWorktrees.ts";
 
 const git = (cwd: string, args: ReadonlyArray<string>) =>
   Effect.flatMap(VcsProcess.VcsProcess, (process) =>
@@ -187,3 +190,164 @@ it.effect("does nothing on databases that never ran the fork", () =>
     );
   }).pipe(Effect.provide(NodeServices.layer)),
 );
+
+const workspaceFileLayer = NodeSqliteClient.layer({ filename: ":memory:" }).pipe(
+  Layer.merge(WorkspaceRepositories.layer),
+  Layer.provideMerge(NodeServices.layer),
+);
+
+const forkWorkspace = JSON.stringify({
+  folders: [
+    { path: "./api", name: "api" },
+    { path: "./web", name: "web" },
+  ],
+});
+
+/** A project with `api` and `web`, and a thread's container recorded in V2 at `container`. */
+const makeForkThread = Effect.fn("makeForkThread")(function* (input: {
+  readonly threadId: string;
+  readonly projectRoot: string;
+  readonly container: string;
+  /** How many worktrees the fork recorded for the thread; 2 unless set. */
+  readonly forkWorktrees?: number;
+}) {
+  const fileSystem = yield* FileSystem.FileSystem;
+  const path = yield* Path.Path;
+  const sql = yield* SqlClient.SqlClient;
+  for (const name of ["api", "web"]) {
+    yield* fileSystem.makeDirectory(path.join(input.projectRoot, name, ".git"), {
+      recursive: true,
+    });
+    yield* fileSystem.makeDirectory(path.join(input.container, name), { recursive: true });
+  }
+  yield* fileSystem.writeFileString(
+    path.join(input.projectRoot, "team.code-workspace"),
+    forkWorkspace,
+  );
+  yield* fileSystem.writeFileString(
+    WorkspaceRepositories.isolatedRunLayoutPath(input.container),
+    JSON.stringify({
+      repositories: ["api", "web"].map((name) => ({
+        relativePath: name,
+        name,
+        source: path.join(input.projectRoot, name),
+      })),
+    }),
+  );
+  yield* sql`
+    INSERT INTO orchestration_v2_projection_threads (thread_id, project_id, deleted_at, payload_json)
+    VALUES (
+      ${input.threadId},
+      ${input.threadId},
+      NULL,
+      ${JSON.stringify({ worktreePath: input.container })}
+    )
+  `;
+  yield* sql`
+    INSERT INTO projection_projects (project_id, workspace_root)
+    VALUES (${input.threadId}, ${input.projectRoot})
+  `;
+  const forkWorktrees = ["api", "web"].slice(0, input.forkWorktrees ?? 2).map((name) => ({
+    repoRoot: path.join(input.projectRoot, name),
+    worktreePath: path.join(input.container, name),
+  }));
+  yield* sql`
+    INSERT INTO projection_threads (thread_id, worktrees_json)
+    VALUES (${input.threadId}, ${JSON.stringify(forkWorktrees)})
+  `;
+});
+
+const createWorkspaceFileTables = Effect.gen(function* () {
+  const sql = yield* SqlClient.SqlClient;
+  yield* sql`
+    CREATE TABLE orchestration_v2_projection_threads (
+      thread_id TEXT PRIMARY KEY,
+      project_id TEXT NOT NULL,
+      deleted_at TEXT,
+      payload_json TEXT NOT NULL
+    )
+  `;
+  yield* sql`CREATE TABLE projection_projects (project_id TEXT PRIMARY KEY, workspace_root TEXT)`;
+  yield* sql`
+    CREATE TABLE projection_threads (
+      thread_id TEXT PRIMARY KEY,
+      worktrees_json TEXT NOT NULL DEFAULT '[]'
+    )
+  `;
+});
+
+it.effect("writes V2's workspace file for fork threads and keeps the fork's copy", () =>
+  Effect.gen(function* () {
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const baseDir = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-fork-workspace-" });
+    const projectRoot = path.join(baseDir, "team");
+    const container = path.join(baseDir, "worktrees", "project-1", "thread-1");
+    yield* createWorkspaceFileTables;
+    yield* makeForkThread({ threadId: "thread-1", projectRoot, container });
+    // The fork's copy inside the container, pointed at the worktrees.
+    const forkCopy = path.join(container, "team.code-workspace");
+    yield* fileSystem.writeFileString(forkCopy, forkWorkspace);
+
+    assert.strictEqual(yield* writeMultiRepoForkWorkspaceFiles(), 1);
+
+    const written = JSON.parse(
+      yield* fileSystem.readFileString(
+        WorkspaceRepositories.isolatedRunWorkspaceFilePath(container),
+      ),
+    );
+    assert.deepStrictEqual(written.folders, [
+      { path: path.join(container, "api"), name: "api" },
+      { path: path.join(container, "web"), name: "web" },
+    ]);
+    // The pre-V2 build opens the fork's copy, so it stays as it was.
+    assert.strictEqual(yield* fileSystem.readFileString(forkCopy), forkWorkspace);
+    const service = yield* WorkspaceRepositories.WorkspaceRepositories;
+    assert.strictEqual(
+      yield* service.workspaceFile(container),
+      WorkspaceRepositories.isolatedRunWorkspaceFilePath(container),
+    );
+
+    assert.strictEqual(yield* writeMultiRepoForkWorkspaceFiles(), 0);
+  }).pipe(Effect.provide(workspaceFileLayer)),
+);
+
+it.effect("leaves V2 isolated runs that link the project's workspace file alone", () =>
+  Effect.gen(function* () {
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const baseDir = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-fork-workspace-" });
+    const projectRoot = path.join(baseDir, "team");
+    const container = path.join(baseDir, "worktrees", "project-1", "thread-1");
+    yield* createWorkspaceFileTables;
+    yield* makeForkThread({ threadId: "thread-1", projectRoot, container });
+    yield* fileSystem.symlink(
+      path.join(projectRoot, "team.code-workspace"),
+      path.join(container, "team.code-workspace"),
+    );
+
+    assert.strictEqual(yield* writeMultiRepoForkWorkspaceFiles(), 0);
+    assert.isFalse(
+      yield* fileSystem.exists(WorkspaceRepositories.isolatedRunWorkspaceFilePath(container)),
+    );
+  }).pipe(Effect.provide(workspaceFileLayer)),
+);
+
+it.effect("leaves threads the fork gave a single worktree alone", () =>
+  Effect.gen(function* () {
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const baseDir = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-fork-workspace-" });
+    const projectRoot = path.join(baseDir, "team");
+    const container = path.join(baseDir, "worktrees", "project-1", "thread-1");
+    yield* createWorkspaceFileTables;
+    yield* makeForkThread({ threadId: "thread-1", projectRoot, container, forkWorktrees: 1 });
+    // A real file in the container, as a root repository that commits one would leave.
+    yield* fileSystem.writeFileString(path.join(container, "team.code-workspace"), forkWorkspace);
+
+    assert.strictEqual(yield* writeMultiRepoForkWorkspaceFiles(), 0);
+    assert.isFalse(
+      yield* fileSystem.exists(WorkspaceRepositories.isolatedRunWorkspaceFilePath(container)),
+    );
+  }).pipe(Effect.provide(workspaceFileLayer)),
+);
diff --git a/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.ts b/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.ts
index 0a9f15b88042..e661e8c571db 100644
--- a/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.ts
+++ b/apps/server/src/orchestration-v2/legacy/repairMultiRepoForkWorktrees.ts
@@ -19,6 +19,7 @@ import * as Schema from "effect/Schema";
 import * as SqlClient from "effect/sql/SqlClient";
 
 import * as ServerConfig from "../../config.ts";
+import { writeIsolatedRunWorkspaceFile } from "../../git/isolatedRunWorkspaceFile.ts";
 import * as WorkspaceRepositories from "../../workspace/WorkspaceRepositories.ts";
 import * as ThreadManagement from "../ThreadManagementService.ts";
 
@@ -108,3 +109,92 @@ export const repairMultiRepoForkWorktrees = Effect.fn("repairMultiRepoForkWorktr
   }
   return repaired;
 });
+
+/**
+ * Gives repaired fork threads the workspace file V2 writes beside a new isolated run.
+ *
+ * The fork kept its copy inside the container, so V2's "Open in" fell back to the bare folder.
+ * This writes V2's own file from the project's workspace file. The fork's copy stays, because
+ * the pre-V2 build opens it and a database can still go back to that build. Threads that
+ * already have the file are skipped, so this runs once per thread.
+ */
+export const writeMultiRepoForkWorkspaceFiles = Effect.fn("writeMultiRepoForkWorkspaceFiles")(
+  function* () {
+    const sql = yield* SqlClient.SqlClient;
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const workspaceRepositories = yield* WorkspaceRepositories.WorkspaceRepositories;
+
+    const columns = yield* sql<{ readonly name: string }>`PRAGMA table_info(projection_threads)`;
+    if (!columns.some((column) => column.name === "worktrees_json")) return 0;
+
+    // Only threads the fork gave several worktrees can hold its copy, so a database that
+    // never ran the fork touches no files.
+    const rows = yield* sql<{
+      readonly thread_id: string;
+      readonly worktree_path: string;
+      readonly workspace_root: string;
+    }>`
+      SELECT
+        thread.thread_id,
+        json_extract(thread.payload_json, '$.worktreePath') AS worktree_path,
+        project.workspace_root
+      FROM orchestration_v2_projection_threads AS thread
+      INNER JOIN projection_projects AS project ON project.project_id = thread.project_id
+      INNER JOIN projection_threads AS fork ON fork.thread_id = thread.thread_id
+      WHERE thread.deleted_at IS NULL
+        AND json_extract(thread.payload_json, '$.worktreePath') IS NOT NULL
+        AND CASE WHEN json_valid(fork.worktrees_json)
+          THEN json_array_length(fork.worktrees_json) ELSE 0 END > 1
+    `;
+
+    // Only the fork left a real workspace file in a container; V2 links the project's in.
+    const holdsForkCopy = (container: string) =>
+      fileSystem.readDirectory(container).pipe(
+        Effect.flatMap((names) => {
+          const held = names.filter((name) =>
+            name.endsWith(WorkspaceRepositories.CODE_WORKSPACE_EXTENSION),
+          );
+          if (held.length !== 1) return Effect.succeed(false);
+          return fileSystem.readLink(path.join(container, held[0]!)).pipe(
+            Effect.as(false),
+            Effect.orElseSucceed(() => true),
+          );
+        }),
+        Effect.orElseSucceed(() => false),
+      );
+
+    let written = 0;
+    for (const row of rows) {
+      const container = row.worktree_path;
+      const target = WorkspaceRepositories.isolatedRunWorkspaceFilePath(container);
+      if (yield* fileSystem.exists(target).pipe(Effect.orElseSucceed(() => true))) continue;
+      const layout = yield* workspaceRepositories.readIsolatedRun(container);
+      if (layout === null || !(yield* holdsForkCopy(container))) continue;
+      const projectWorkspaceFile = yield* workspaceRepositories.workspaceFile(row.workspace_root);
+      if (projectWorkspaceFile === null) continue;
+
+      yield* writeIsolatedRunWorkspaceFile({
+        projectWorkspaceFile,
+        container,
+        repositories: layout.repositories.map((repository) => ({
+          source: repository.source,
+          worktree: path.resolve(container, repository.relativePath),
+        })),
+      }).pipe(
+        Effect.tap(() =>
+          Effect.sync(() => {
+            written += 1;
+          }),
+        ),
+        Effect.catch((cause) =>
+          Effect.logWarning("Could not write a multi-repo fork thread's workspace file", {
+            threadId: row.thread_id,
+            cause,
+          }),
+        ),
+      );
+    }
+    return written;
+  },
+);
diff --git a/apps/server/src/serverRuntimeStartup.autoPull.test.ts b/apps/server/src/serverRuntimeStartup.autoPull.test.ts
index 67bff5023436..3ec169a7a15f 100644
--- a/apps/server/src/serverRuntimeStartup.autoPull.test.ts
+++ b/apps/server/src/serverRuntimeStartup.autoPull.test.ts
@@ -34,6 +34,7 @@ import * as ServerRuntimeStartup from "./serverRuntimeStartup.ts";
 import * as ServerSettings from "./serverSettings.ts";
 import * as AnalyticsService from "./telemetry/AnalyticsService.ts";
 import * as GitVcsDriver from "./vcs/GitVcsDriver.ts";
+import * as WorkspaceRepositories from "./workspace/WorkspaceRepositories.ts";
 
 it.effect("parks automatic pull until activation without delaying command readiness", () =>
   Effect.scoped(
@@ -140,6 +141,7 @@ it.effect("parks automatic pull until activation without delaying command readin
           listShells: () => Effect.succeed(snapshot.projects),
         }),
         Layer.mock(ProjectService.ProjectService)({ snapshot: Effect.succeed(snapshot) }),
+        Layer.mock(WorkspaceRepositories.WorkspaceRepositories)({}),
         Layer.mock(ThreadManagement.ThreadManagementService)({
           getShellSnapshot: () =>
             Effect.succeed({
diff --git a/apps/server/src/serverRuntimeStartup.ts b/apps/server/src/serverRuntimeStartup.ts
index 5ae83d8cdfdd..cd34a1234181 100644
--- a/apps/server/src/serverRuntimeStartup.ts
+++ b/apps/server/src/serverRuntimeStartup.ts
@@ -32,7 +32,10 @@ import * as Keybindings from "./keybindings.ts";
 import * as ExternalLauncher from "./process/externalLauncher.ts";
 import * as EffectWorker from "./orchestration-v2/EffectWorker.ts";
 import * as LegacyV1ThreadImporter from "./orchestration-v2/legacy/LegacyV1ThreadImporter.ts";
-import { repairMultiRepoForkWorktrees } from "./orchestration-v2/legacy/repairMultiRepoForkWorktrees.ts";
+import {
+  repairMultiRepoForkWorktrees,
+  writeMultiRepoForkWorkspaceFiles,
+} from "./orchestration-v2/legacy/repairMultiRepoForkWorktrees.ts";
 import * as Orchestrator from "./orchestration-v2/Orchestrator.ts";
 import * as ProviderRuntimeRecovery from "./orchestration-v2/ProviderRuntimeRecoveryService.ts";
 import * as ProviderSessionManager from "./orchestration-v2/ProviderSessionManager.ts";
@@ -553,6 +556,19 @@ const make = (options?: StartupOptions) =>
           ),
         ),
       );
+      yield* runStartupPhase(
+        "orchestration-v2.legacy-v1.multi-repo-fork-workspace-files",
+        writeMultiRepoForkWorkspaceFiles().pipe(
+          Effect.tap((written) =>
+            written === 0
+              ? Effect.void
+              : Effect.logInfo("Wrote workspace files for multi-repo fork threads", { written }),
+          ),
+          Effect.catch((cause) =>
+            Effect.logWarning("Failed to write multi-repo fork thread workspace files", { cause }),
+          ),
+        ),
+      );
       // Runs after activation: the status check fetches every enabled project's
       // remote, and awaiting it here held command readiness for that long.
       yield* runStartupPhase(