Default new worktrees to the upstream branch (#2848)

* fix(workspaces): default new worktrees to upstream refs

Use the daemon-resolved upstream as the untouched starting ref so unpushed local commits do not leak into new workspaces. Preserve exact base identity for fork remotes while keeping local-first behavior across version drift.

* fix(workspaces): preserve exact base refs in git actions

Resolve accepted display aliases back to the stored ref before comparisons and updates. Fail closed when a non-origin remote base has no explicit mutable merge target.

* fix(workspaces): reject conflicting qualified base refs

Display aliases remain accepted for compatibility, but a qualified ref carries remote identity and must not be canonicalized to a different stored upstream.

* test(server): make upstream fixtures portable

Keep the checkout-status fixture aligned with the optional upstream field, and select main explicitly when cloning a bare test remote whose default HEAD varies by platform.

* fix(workspaces): preserve exact upstream refs

Qualified remote refs now fail closed when pruned instead of switching lineage. Metadata accepts Git-valid upstream names rather than applying a narrower character whitelist.

* fix(workspaces): preserve qualified local base refs

Local tracking branches are exact upstream identities too. Keep heuristics only for legacy unqualified metadata so origin cannot replace a stored refs/heads base.

docs/development.md

@@ -280,11 +280,18 @@ for machine-readable output.
 
 ## Worktree starting refs
 
-The New workspace branch picker treats local and `origin/*` refs as distinct starting points when
+A new worktree starts from the current branch's upstream, or the local branch when it has no
-they differ. Local `main` is sent as `refs/heads/main`; remote `origin/main` is sent as
+upstream. This keeps unpushed local commits out of new workspaces by default. The picker collapses
-`refs/remotes/origin/main`. Matching local/remote refs collapse to one local row. Unqualified refs
+identical refs; divergent local or non-origin refs remain explicit, qualified choices.
-from older clients resolve local-first, then fall back to `origin`. Worktrees inherit committed Git
+
-state only; uncommitted source-checkout changes are not copied.
+The daemon sends the exact upstream ref because the remote and branch names cannot be inferred.
+Worktrees retain that ref for comparisons and updates from base while exposing its branch name to
+the UI. Merging into base requires a mutable local target: `origin/main` maps to local `main`, while
+another remote fails closed until the worktree records an explicit local target. Older daemons omit
+the optional field and retain the previous local-first behavior; older worktree metadata without the
+exact ref also resolves through its stored branch name.
+
+Worktrees inherit committed Git state only; uncommitted source-checkout changes are not copied.
 
 ## paseo.json service scripts
 

packages/app/e2e/browser/new-workspace.spec.ts

@@ -24,6 +24,10 @@ import {
   openProjectViaDaemon,
   openStartingRefPicker,
   pasteGithubPrUrl,
+  captureStartingRefPicker,
+  expectStartingRefRows,
+  startingRefRow,
+  submitNewWorkspaceEmpty,
   searchAndSelectBranchInPicker,
   selectBranchInPicker,
   selectGitHubPrInPicker,
@@ -31,7 +35,14 @@ import {
   selectWorkspaceIsolation,
   submitNewWorkspacePrompt,
 } from "../support/helpers/new-workspace";
-import { createTempGitRepo, readWorktreeBranchInfo } from "../support/helpers/workspace";
+import {
+  commitLocalOnly,
+  createTempGitRepo,
+  readRepoRef,
+  readWorktreeBaseMetadata,
+  readWorktreeBranchInfo,
+  trackForkUpstream,
+} from "../support/helpers/workspace";
 import {
   createLocalGithubPrFixture,
   cloneGithubRepoDefaultBranchOnly,
@@ -743,6 +754,142 @@ test.describe("New workspace flow", () => {
     }
   });
 
+  // The starting ref the daemon actually cuts from is the thing that broke: the picker said
+  // one ref and the worktree was created from another. Every assertion here reads the
+  // created worktree's commits or its recorded base, never the trigger text alone.
+  test.describe("default starting ref", () => {
+    async function openWorktreeComposerForRepo(
+      page: import("@playwright/test").Page,
+      repoPath: string,
+    ) {
+      const openedProject = await openProjectViaDaemon(client, repoPath);
+      localWorkspaceIds.add(openedProject.workspaceId);
+
+      await gotoAppShell(page);
+      await waitForSidebarHydration(page);
+      await openNewWorkspaceComposer(page, {
+        projectKey: openedProject.projectKey,
+        projectDisplayName: openedProject.projectDisplayName,
+      });
+      await selectWorkspaceIsolation(page, "worktree");
+      return openedProject;
+    }
+
+    async function createWorktreeAndRead(
+      page: import("@playwright/test").Page,
+      openedProject: Awaited<ReturnType<typeof openProjectViaDaemon>>,
+    ) {
+      await submitNewWorkspaceEmpty(page);
+      const createdWorkspace = await assertNewWorkspaceSidebarAndHeader(page, {
+        serverId: getServerId(),
+        client,
+        previousWorkspaceId: openedProject.workspaceId,
+        projectDisplayName: openedProject.projectDisplayName,
+      });
+      createdWorktreeDirectories.add(createdWorkspace.workspaceDirectory);
+      return {
+        ...createdWorkspace,
+        branchInfo: await readWorktreeBranchInfo({
+          worktreePath: createdWorkspace.workspaceDirectory,
+        }),
+      };
+    }
+
+    test("branches off the upstream when the local branch is ahead and the picker is untouched", async ({
+      page,
+    }) => {
+      const tempRepo = await createTempGitRepo("ref-default-ahead-", { withRemote: true });
+
+      try {
+        const originHead = readRepoRef(tempRepo.path, "refs/remotes/origin/main");
+        commitLocalOnly(tempRepo.path, "one");
+        const localHead = commitLocalOnly(tempRepo.path, "two");
+
+        const openedProject = await openWorktreeComposerForRepo(page, tempRepo.path);
+        const created = await createWorktreeAndRead(page, openedProject);
+
+        expect(created.branchInfo.hasAncestor(originHead)).toBe(true);
+        expect(created.branchInfo.hasAncestor(localHead)).toBe(false);
+      } finally {
+        await tempRepo.cleanup();
+      }
+    });
+
+    test("branches off the local ref when the local row is chosen explicitly", async ({
+      page,
+    }, testInfo) => {
+      const tempRepo = await createTempGitRepo("ref-default-local-pick-", { withRemote: true });
+
+      try {
+        commitLocalOnly(tempRepo.path, "one");
+        const localHead = commitLocalOnly(tempRepo.path, "two");
+
+        const openedProject = await openWorktreeComposerForRepo(page, tempRepo.path);
+
+        await openStartingRefPicker(page);
+        await expectStartingRefRows(page, [
+          "main, origin branch",
+          "main, local branch, 2 commits ahead of origin main",
+        ]);
+        const screenshotPath = testInfo.outputPath("ref-picker-local-ahead.png");
+        await captureStartingRefPicker(page, screenshotPath);
+        await testInfo.attach("Ref picker: local ahead of upstream", {
+          path: screenshotPath,
+          contentType: "image/png",
+        });
+        await startingRefRow(page, "main, local branch, 2 commits ahead of origin main").click();
+        await expectPickerSelected(page, "main (local)");
+
+        const created = await createWorktreeAndRead(page, openedProject);
+        expect(created.branchInfo.hasAncestor(localHead)).toBe(true);
+      } finally {
+        await tempRepo.cleanup();
+      }
+    });
+
+    test("branches off a fork's upstream remote and records the branch name", async ({
+      page,
+    }, testInfo) => {
+      const tempRepo = await createTempGitRepo("ref-default-fork-", { withRemote: true });
+
+      try {
+        const upstreamHead = await trackForkUpstream(tempRepo.path);
+        const originHead = readRepoRef(tempRepo.path, "refs/remotes/origin/main");
+
+        const openedProject = await openWorktreeComposerForRepo(page, tempRepo.path);
+
+        await openStartingRefPicker(page);
+        // Branch suggestions only know about origin, so the upstream the fork actually
+        // tracks gets its own row rather than silently sharing origin's. Two rows reading
+        // "main" is the ambiguity this whole change exists to remove.
+        await expectStartingRefRows(page, [
+          "main (upstream), upstream branch",
+          "main, origin branch",
+        ]);
+        await expectPickerSelected(page, "main (upstream)");
+        const screenshotPath = testInfo.outputPath("ref-picker-fork.png");
+        await captureStartingRefPicker(page, screenshotPath);
+        await testInfo.attach("Ref picker: fork tracking upstream/main", {
+          path: screenshotPath,
+          contentType: "image/png",
+        });
+        await closeBranchPicker(page);
+
+        const created = await createWorktreeAndRead(page, openedProject);
+
+        expect(created.branchInfo.hasAncestor(upstreamHead)).toBe(true);
+        expect(upstreamHead).not.toBe(originHead);
+        // The name is what the UI shows; the ref is what resolves back to this commit.
+        expect(await readWorktreeBaseMetadata(created.workspaceDirectory)).toEqual({
+          baseRefName: "main",
+          baseRef: "refs/remotes/upstream/main",
+        });
+      } finally {
+        await tempRepo.cleanup();
+      }
+    });
+  });
+
   test("branch picker opens via keyboard and selects the filtered option on Enter", async ({
     page,
   }) => {

packages/app/e2e/support/helpers/new-workspace.ts

@@ -348,6 +348,23 @@ export async function searchAndSelectBranchInPicker(page: Page, name: string): P
   await selectBranchInPicker(page, name);
 }
 
+// Ref picker rows are named for a user: "main, origin branch" is the upstream copy and
+// "main, local branch, 2 commits ahead of origin main" is the local one.
+export function startingRefRow(page: Page, accessibleName: string) {
+  return page.getByRole("button", { name: accessibleName, exact: true });
+}
+
+export async function expectStartingRefRows(page: Page, accessibleNames: string[]): Promise<void> {
+  for (const name of accessibleNames) {
+    await expect(startingRefRow(page, name)).toBeVisible({ timeout: 30_000 });
+  }
+}
+
+export async function captureStartingRefPicker(page: Page, screenshotPath: string): Promise<void> {
+  await expect(page.getByTestId("combobox-desktop-container")).toBeVisible({ timeout: 30_000 });
+  await page.getByTestId("combobox-desktop-container").screenshot({ path: screenshotPath });
+}
+
 export async function selectGitHubPrInPicker(page: Page, number: number): Promise<void> {
   const prRow = page.getByTestId(`new-workspace-ref-picker-pr-${number}`);
   await expect(prRow).toBeVisible({ timeout: 30_000 });

packages/app/e2e/support/helpers/workspace.ts

@@ -1,5 +1,5 @@
 import { execSync } from "node:child_process";
-import { mkdtemp, writeFile, rm, mkdir, realpath } from "node:fs/promises";
+import { mkdtemp, readFile, writeFile, rm, mkdir, realpath } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import path from "node:path";
 
@@ -159,6 +159,80 @@ export async function createTempDirectory(prefix = "paseo-e2e-dir-"): Promise<Te
   };
 }
 
+/**
+ * A commit that exists only in the local checkout. The whole point of defaulting a new
+ * worktree to the upstream is that these commits do not leak into it.
+ */
+export function commitLocalOnly(repoPath: string, marker: string): string {
+  execSync(`git commit --allow-empty -m ${JSON.stringify(`local only ${marker}`)}`, {
+    cwd: repoPath,
+    stdio: "ignore",
+  });
+  return execSync("git rev-parse HEAD", { cwd: repoPath, stdio: "pipe" }).toString().trim();
+}
+
+/**
+ * A fork checkout: `origin` is the fork, `upstream` is the source repo, and the current
+ * branch tracks `upstream/main`. Upstream carries a commit origin does not, so a worktree
+ * based on the wrong remote is provable rather than coincidentally identical.
+ */
+export async function trackForkUpstream(repoPath: string): Promise<string> {
+  const upstreamDir = path.join(repoPath, "upstream.git");
+  const upstreamClone = await mkdtemp(path.join(await resolveTempRoot(), "paseo-e2e-upstream-"));
+  await mkdir(upstreamDir, { recursive: true });
+  execSync(`git init --bare -b main ${upstreamDir}`, { cwd: repoPath, stdio: "ignore" });
+  execSync(`git remote add upstream ${upstreamDir}`, { cwd: repoPath, stdio: "ignore" });
+  execSync("git push upstream main", { cwd: repoPath, stdio: "ignore" });
+
+  execSync(`git clone ${upstreamDir} ${upstreamClone}`, { stdio: "ignore" });
+  execSync('git config user.email "e2e@paseo.test"', { cwd: upstreamClone, stdio: "ignore" });
+  execSync('git config user.name "Paseo E2E"', { cwd: upstreamClone, stdio: "ignore" });
+  execSync("git config commit.gpgsign false", { cwd: upstreamClone, stdio: "ignore" });
+  execSync('git commit --allow-empty -m "upstream only"', {
+    cwd: upstreamClone,
+    stdio: "ignore",
+  });
+  execSync("git push origin main", { cwd: upstreamClone, stdio: "ignore" });
+  await rm(upstreamClone, { recursive: true, force: true });
+
+  execSync("git fetch upstream", { cwd: repoPath, stdio: "ignore" });
+  execSync("git branch --set-upstream-to=upstream/main main", {
+    cwd: repoPath,
+    stdio: "ignore",
+  });
+  return execSync("git rev-parse refs/remotes/upstream/main", { cwd: repoPath, stdio: "pipe" })
+    .toString()
+    .trim();
+}
+
+export function readRepoRef(repoPath: string, ref: string): string {
+  return execSync(`git rev-parse ${JSON.stringify(ref)}`, { cwd: repoPath, stdio: "pipe" })
+    .toString()
+    .trim();
+}
+
+/**
+ * The base identity the daemon recorded in worktree.json: the display name the UI reads back,
+ * and the exact ref every comparison and action resolves through.
+ */
+export async function readWorktreeBaseMetadata(
+  worktreePath: string,
+): Promise<{ baseRefName: string; baseRef?: string }> {
+  const gitDir = execSync("git rev-parse --absolute-git-dir", { cwd: worktreePath, stdio: "pipe" })
+    .toString()
+    .trim();
+  const metadata = JSON.parse(
+    await readFile(path.join(gitDir, "paseo", "worktree.json"), "utf8"),
+  ) as { baseRefName?: string; baseRef?: string };
+  if (!metadata.baseRefName) {
+    throw new Error(`worktree.json has no baseRefName: ${worktreePath}`);
+  }
+  return {
+    baseRefName: metadata.baseRefName,
+    ...(metadata.baseRef ? { baseRef: metadata.baseRef } : {}),
+  };
+}
+
 export async function readWorktreeBranchInfo({ worktreePath }: { worktreePath: string }): Promise<{
   currentBranch: string;
   hasAncestor: (ref: string) => boolean;

packages/app/src/screens/new-workspace-picker-item.test.ts

@@ -1,11 +1,12 @@
 import { describe, expect, it } from "vitest";
 import type { ForgeSearchItem } from "@getpaseo/protocol/messages";
-import type { CheckoutStatusPayload } from "@/git/checkout-status-cache";
 import {
+  type BranchPickerDetail,
   branchPickerOptionId,
   buildBranchPickerItems,
+  buildPickerOptionData,
+  defaultBasePickerItem,
   pickerItemToCheckoutRequest,
-  resolveCheckoutRequest,
   type PickerItem,
 } from "./new-workspace-picker-item";
 
@@ -104,7 +105,7 @@ describe("pickerItemToCheckoutRequest", () => {
 });
 
 describe("buildBranchPickerItems", () => {
-  it("hides the origin duplicate when local and origin match", () => {
+  it("keeps a single origin row when local and origin match", () => {
     expect(
       buildBranchPickerItems([
         {
@@ -120,14 +121,14 @@ describe("buildBranchPickerItems", () => {
       {
         kind: "branch",
         name: "main",
-        refName: "refs/heads/main",
+        refName: "refs/remotes/origin/main",
-        accessibilityLabel: "main, local branch, up to date with origin main",
+        accessibilityLabel: "main, origin branch",
         committerDate: 10,
       },
     ]);
   });
 
-  it("creates compact local and origin rows when the refs differ", () => {
+  it("puts the origin row first and disambiguates the local row when the refs differ", () => {
     expect(
       buildBranchPickerItems([
         {
@@ -143,17 +144,16 @@ describe("buildBranchPickerItems", () => {
       {
         kind: "branch",
         name: "main",
-        refName: "refs/heads/main",
+        refName: "refs/remotes/origin/main",
-        divergenceLabel: "+3 −2",
+        accessibilityLabel: "main, origin branch",
-        accessibilityLabel: "main, local branch, 3 commits ahead and 2 behind origin main",
         committerDate: 10,
       },
       {
         kind: "branch",
-        name: "origin/main",
+        name: "main (local)",
-        refName: "refs/remotes/origin/main",
+        refName: "refs/heads/main",
-        divergenceLabel: "+2 −3",
+        divergenceLabel: "+3 −2",
-        accessibilityLabel: "origin main, 2 commits ahead and 3 behind local main",
+        accessibilityLabel: "main, local branch, 3 commits ahead and 2 behind origin main",
         committerDate: 10,
       },
     ]);
@@ -172,9 +172,30 @@ describe("buildBranchPickerItems", () => {
     ).toEqual([
       {
         kind: "branch",
-        name: "origin/release",
+        name: "release",
         refName: "refs/remotes/origin/release",
-        accessibilityLabel: "origin release, origin branch",
+        accessibilityLabel: "release, origin branch",
+        committerDate: 5,
+      },
+    ]);
+  });
+
+  it("keeps the plain name for a local-only branch", () => {
+    expect(
+      buildBranchPickerItems([
+        {
+          name: "scratch",
+          committerDate: 5,
+          hasLocal: true,
+          hasRemote: false,
+        },
+      ]),
+    ).toEqual([
+      {
+        kind: "branch",
+        name: "scratch",
+        refName: "refs/heads/scratch",
+        accessibilityLabel: "scratch, local branch",
         committerDate: 5,
       },
     ]);
@@ -194,15 +215,15 @@ describe("buildBranchPickerItems", () => {
       {
         kind: "branch",
         name: "main",
-        refName: "refs/heads/main",
+        refName: "refs/remotes/origin/main",
-        accessibilityLabel: "main, local branch",
+        accessibilityLabel: "main, origin branch",
         committerDate: 10,
       },
       {
         kind: "branch",
-        name: "origin/main",
+        name: "main (local)",
-        refName: "refs/remotes/origin/main",
+        refName: "refs/heads/main",
-        accessibilityLabel: "origin main, origin branch",
+        accessibilityLabel: "main, local branch",
         committerDate: 10,
       },
     ]);
@@ -221,38 +242,101 @@ describe("buildBranchPickerItems", () => {
   });
 });
 
-describe("resolveCheckoutRequest", () => {
+const mainRow: BranchPickerDetail = {
-  const checkoutStatus = {
+  name: "main",
-    currentBranch: "feature/current",
+  committerDate: 10,
-  } as CheckoutStatusPayload;
+  hasLocal: true,
+  hasRemote: true,
+  localAhead: 2,
+  localBehind: 0,
+};
 
-  it("branches from the loaded current branch when nothing was picked", () => {
+describe("buildPickerOptionData", () => {
-    expect(resolveCheckoutRequest(null, checkoutStatus)).toEqual({
+  it("marks origin and keeps an ahead local main explicit", () => {
-      action: "branch-off",
+    const baseItem = defaultBasePickerItem({
-      refName: "feature/current",
+      currentBranch: "main",
+      upstreamRef: "refs/remotes/origin/main",
     });
+    const data = buildPickerOptionData({ branchDetails: [mainRow], prItems: [], baseItem });
+
+    expect(data.options.map((option) => option.label)).toEqual(["main", "main (local)"]);
+    expect(data.selectedOptionId).toBe(branchPickerOptionId("refs/remotes/origin/main"));
   });
 
-  it("prefers an explicit picker selection", () => {
+  it("adds and disambiguates a fork upstream absent from branch suggestions", () => {
-    expect(
+    const baseItem = defaultBasePickerItem({
-      resolveCheckoutRequest(
+      currentBranch: "main",
-        {
+      upstreamRef: "refs/remotes/upstream/main",
-          kind: "branch",
-          name: "feature/picked",
-          refName: "refs/heads/feature/picked",
-          accessibilityLabel: "feature/picked, local branch",
-        },
-        checkoutStatus,
-      ),
-    ).toEqual({
-      action: "branch-off",
-      refName: "refs/heads/feature/picked",
     });
+    const data = buildPickerOptionData({
+      branchDetails: [{ ...mainRow, localAhead: 0, localBehind: 0 }],
+      prItems: [],
+      baseItem,
+    });
+
+    expect(data.options.map((option) => option.label)).toEqual(["main (upstream)", "main"]);
+    expect(data.selectedOptionId).toBe(branchPickerOptionId("refs/remotes/upstream/main"));
   });
 
-  it("preserves the server-default intent for a detached checkout", () => {
+  it("marks a visible row on an old daemon when local and origin are in sync", () => {
+    const baseItem = defaultBasePickerItem({ currentBranch: "main" });
+    const data = buildPickerOptionData({
+      branchDetails: [{ ...mainRow, localAhead: 0, localBehind: 0 }],
+      prItems: [],
+      baseItem,
+    });
+
+    expect(data.options.map((option) => option.label)).toEqual(["main (local)", "main"]);
+    expect(data.selectedOptionId).toBe(branchPickerOptionId("refs/heads/main"));
+  });
+
+  it("keeps an explicit local selection marked", () => {
+    const baseItem: PickerItem = {
+      kind: "branch",
+      name: "main (local)",
+      refName: "refs/heads/main",
+      accessibilityLabel: "main, local branch",
+    };
+    const data = buildPickerOptionData({
+      branchDetails: [mainRow],
+      prItems: [],
+      baseItem,
+    });
+    const selected = data.itemById.get(data.selectedOptionId) ?? null;
+    expect(pickerItemToCheckoutRequest(selected)).toEqual({
+      action: "branch-off",
+      refName: "refs/heads/main",
+    });
+  });
+});
+
+describe("defaultBasePickerItem", () => {
+  it("uses origin when the current branch tracks origin", () => {
     expect(
-      resolveCheckoutRequest(null, { ...checkoutStatus, currentBranch: null }),
+      defaultBasePickerItem({
-    ).toBeUndefined();
+        currentBranch: "main",
+        upstreamRef: "refs/remotes/origin/main",
+      }),
+    ).toMatchObject({ refName: "refs/remotes/origin/main", name: "main" });
+  });
+
+  it("uses the exact non-origin upstream", () => {
+    expect(
+      defaultBasePickerItem({
+        currentBranch: "main",
+        upstreamRef: "refs/remotes/upstream/main",
+      }),
+    ).toMatchObject({ refName: "refs/remotes/upstream/main", name: "main" });
+  });
+
+  it("keeps old-daemon behavior local", () => {
+    expect(defaultBasePickerItem({ currentBranch: "main" })).toMatchObject({
+      refName: "refs/heads/main",
+      name: "main",
+    });
+  });
+
+  it("has no default for detached HEAD", () => {
+    expect(defaultBasePickerItem({ currentBranch: null })).toBeNull();
   });
 });

packages/app/src/screens/new-workspace-picker-item.ts

@@ -1,6 +1,7 @@
 import type { CreatePaseoWorktreeInput } from "@getpaseo/client/internal/daemon-client";
 import type { ForgeSearchItem } from "@getpaseo/protocol/messages";
-import type { CheckoutStatusPayload } from "@/git/checkout-status-cache";
+import type { ComboboxOptionModel } from "@/components/ui/combobox-options";
+import { getForgePresentation } from "@/git/forge";
 
 export interface BranchPickerDetail {
   name: string;
@@ -31,6 +32,8 @@ export type PickerCheckoutRequest = Pick<
 >;
 
 const BRANCH_OPTION_PREFIX = "branch:";
+const PR_OPTION_PREFIX = "github-pr:";
+const REMOTE_TRACKING_PREFIX = "refs/remotes/";
 
 export function branchPickerOptionId(refName: string): string {
   return `${BRANCH_OPTION_PREFIX}${refName}`;
@@ -82,11 +85,27 @@ export function buildBranchPickerItems(details: readonly BranchPickerDetail[]):
     const localBehind = detail.localBehind;
     const hasDivergence =
       hasLocal && hasRemote && localAhead !== undefined && localBehind !== undefined;
+    const refsDiffer = hasDivergence && (localAhead > 0 || localBehind > 0);
+    // One row when the two refs point at the same commit, two rows when they differ or
+    // when the divergence is unknown.
+    const showsBothRefs = hasLocal && hasRemote && (!hasDivergence || refsDiffer);
 
-    if (hasLocal) {
+    // The origin row goes first because it is the default base, and it never states
-      const localItem: Extract<PickerItem, { kind: "branch" }> = {
+    // divergence: it is the reference point the local row is measured against.
+    if (hasRemote) {
+      items.push({
         kind: "branch",
         name: detail.name,
+        refName: `refs/remotes/origin/${detail.name}`,
+        accessibilityLabel: `${detail.name}, origin branch`,
+        committerDate: detail.committerDate,
+      });
+    }
+
+    if (hasLocal && (showsBothRefs || !hasRemote)) {
+      const localItem: Extract<PickerItem, { kind: "branch" }> = {
+        kind: "branch",
+        name: showsBothRefs ? `${detail.name} (local)` : detail.name,
         refName: `refs/heads/${detail.name}`,
         accessibilityLabel: `${detail.name}, local branch`,
         committerDate: detail.committerDate,
@@ -101,33 +120,64 @@ export function buildBranchPickerItems(details: readonly BranchPickerDetail[]):
       }
       items.push(localItem);
     }
-
-    const refsDiffer = hasDivergence && (localAhead > 0 || localBehind > 0);
-    if (hasRemote && (!hasLocal || !hasDivergence || refsDiffer)) {
-      const remoteAhead = hasDivergence ? localBehind : 0;
-      const remoteBehind = hasDivergence ? localAhead : 0;
-      const remoteItem: Extract<PickerItem, { kind: "branch" }> = {
-        kind: "branch",
-        name: `origin/${detail.name}`,
-        refName: `refs/remotes/origin/${detail.name}`,
-        accessibilityLabel: `origin ${detail.name}, origin branch`,
-        committerDate: detail.committerDate,
-      };
-      if (hasDivergence) {
-        remoteItem.divergenceLabel = divergenceLabel(remoteAhead, remoteBehind);
-        remoteItem.accessibilityLabel = `origin ${detail.name}, ${divergenceAccessibility(
-          remoteAhead,
-          remoteBehind,
-          `local ${detail.name}`,
-        )}`;
-      }
-      items.push(remoteItem);
-    }
   }
 
   return items;
 }
 
+export interface BaseRefCheckoutStatus {
+  currentBranch: string | null;
+  upstreamRef?: string | null;
+}
+
+// Display only. The exact ref is what every request carries; this is just how a ref reads in
+// a row label, so "refs/remotes/origin/other-name" shows as "other-name".
+function branchNameFromRef(refName: string): string {
+  if (refName.startsWith("refs/heads/")) return refName.slice("refs/heads/".length);
+  if (refName.startsWith(REMOTE_TRACKING_PREFIX)) {
+    const remainder = refName.slice(REMOTE_TRACKING_PREFIX.length);
+    const separator = remainder.indexOf("/");
+    return separator === -1 ? remainder : remainder.slice(separator + 1);
+  }
+  return refName;
+}
+
+// Where a ref lives, for disambiguating two rows that would otherwise read the same.
+function refQualifier(refName: string): string | null {
+  if (refName.startsWith("refs/heads/")) return "local";
+  if (refName.startsWith(REMOTE_TRACKING_PREFIX)) {
+    const remainder = refName.slice(REMOTE_TRACKING_PREFIX.length);
+    const separator = remainder.indexOf("/");
+    return separator === -1 ? null : remainder.slice(0, separator);
+  }
+  return null;
+}
+
+// The one owner of "what do we branch off when the user picked nothing". The checkmarked
+// row, the trigger label, and the created ref all read this; computing it twice is how the
+// picker once showed local main while branching off something else.
+//
+// The upstream wins when the branch has one, because branching off the local ref silently
+// carries unpushed commits into the new workspace. The daemon sends the resolved ref rather
+// than a remote name, so a fork tracking upstream/main branches from upstream/main.
+export function defaultBasePickerItem(status: BaseRefCheckoutStatus): PickerItem | null {
+  const currentBranch = status.currentBranch;
+  if (!currentBranch) return null;
+  // COMPAT(checkoutUpstreamRef): added in v0.2.6, remove after 2027-02-01 once the daemon
+  // floor sends upstreamRef. Daemons that predate it omit the field, which lands on the
+  // local ref — the base those daemons always used.
+  const refName = status.upstreamRef ?? `refs/heads/${currentBranch}`;
+  // The upstream branch can be named differently from the local one, so the row reads the
+  // ref rather than the branch the user happens to be on.
+  const name = branchNameFromRef(refName);
+  return {
+    kind: "branch",
+    name,
+    refName,
+    accessibilityLabel: status.upstreamRef ? `${name}, upstream branch` : `${name}, local branch`,
+  };
+}
+
 export function pickerItemToCheckoutRequest(
   item: PickerItem | null,
 ): PickerCheckoutRequest | undefined {
@@ -159,15 +209,98 @@ export function pickerItemToCheckoutRequest(
   }
 }
 
-export function resolveCheckoutRequest(
+export function prPickerOptionId(number: number): string {
-  selectedItem: PickerItem | null,
+  return `${PR_OPTION_PREFIX}${number}`;
-  checkoutStatus: CheckoutStatusPayload,
+}
-): PickerCheckoutRequest | undefined {
+
-  const selectedCheckoutRequest = pickerItemToCheckoutRequest(selectedItem);
+export function pickerOptionId(item: PickerItem): string {
-  if (selectedCheckoutRequest) return selectedCheckoutRequest;
+  return item.kind === "branch"
-  if (!checkoutStatus.currentBranch) return undefined;
+    ? branchPickerOptionId(item.refName)
+    : prPickerOptionId(item.item.number);
+}
+
+function formatPrLabel(item: Pick<ForgeSearchItem, "forge" | "number" | "title">): string {
+  const presentation = getForgePresentation(item.forge ?? "github");
+  return `${presentation.numberPrefix}${item.number} ${item.title}`;
+}
+
+export function pickerItemLabel(item: PickerItem): string {
+  return item.kind === "branch" ? item.name : formatPrLabel(item.item);
+}
+
+export interface PickerOptionData {
+  options: ComboboxOptionModel[];
+  itemById: Map<string, PickerItem>;
+  selectedOptionId: string;
+}
+
+interface TimedOption {
+  option: ComboboxOptionModel;
+  timestamp: number;
+}
+
+export function buildPickerOptionData(input: {
+  branchDetails: readonly BranchPickerDetail[];
+  prItems: readonly ForgeSearchItem[];
+  baseItem: PickerItem | null;
+}): PickerOptionData {
+  const itemById = new Map<string, PickerItem>();
+  const timedOptions: TimedOption[] = [];
+
+  for (const branch of buildBranchPickerItems(input.branchDetails)) {
+    if (branch.kind !== "branch") continue;
+    const id = branchPickerOptionId(branch.refName);
+    itemById.set(id, branch);
+    timedOptions.push({
+      option: { id, label: pickerItemLabel(branch) },
+      timestamp: branch.committerDate ?? 0,
+    });
+  }
+
+  for (const pr of input.prItems) {
+    if (!pr.headRefName) continue;
+    const id = prPickerOptionId(pr.number);
+    itemById.set(id, { kind: "github-pr", item: pr });
+    const updatedAtMs = pr.updatedAt ? Date.parse(pr.updatedAt) : 0;
+    const timestamp = Number.isNaN(updatedAtMs) ? 0 : Math.floor(updatedAtMs / 1000);
+    timedOptions.push({ option: { id, label: formatPrLabel(pr) }, timestamp });
+  }
+
+  const baseItem = input.baseItem;
+  if (!baseItem) {
+    timedOptions.sort((a, b) => b.timestamp - a.timestamp);
+    return { options: timedOptions.map((t) => t.option), itemById, selectedOptionId: "" };
+  }
+
+  const selectedOptionId = pickerOptionId(baseItem);
+  if (!itemById.has(selectedOptionId)) {
+    // The label lives on the item, so the row and the trigger read it from the same place.
+    const labeledItem = disambiguate(baseItem, timedOptions);
+    itemById.set(selectedOptionId, labeledItem);
+    timedOptions.push({
+      option: { id: selectedOptionId, label: pickerItemLabel(labeledItem) },
+      // The base sorts first: it is what a workspace is created from unless you pick something.
+      timestamp: Number.POSITIVE_INFINITY,
+    });
+  }
+
+  timedOptions.sort((a, b) => b.timestamp - a.timestamp);
+  return { options: timedOptions.map((t) => t.option), itemById, selectedOptionId };
+}
+
+// Two rows reading "main" would be a coin flip for the user, so the added row says where its
+// ref lives. Only when it collides — a lone row needs no qualifier.
+function disambiguate(item: PickerItem, existing: readonly TimedOption[]): PickerItem {
+  if (item.kind !== "branch") return item;
+  if (!existing.some((entry) => entry.option.label === item.name)) return item;
+  const qualifier = refQualifier(item.refName);
+  if (!qualifier) return item;
+  const name = `${item.name} (${qualifier})`;
   return {
-    action: "branch-off",
+    ...item,
-    refName: checkoutStatus.currentBranch,
+    name,
+    // Accessibility labels are built as `${name}${suffix}`, so re-prefixing keeps the spoken
+    // label and the visible one the same string.
+    accessibilityLabel: `${name}${item.accessibilityLabel.slice(item.name.length)}`,
   };
 }

packages/app/src/screens/new-workspace-screen.tsx

@@ -61,7 +61,6 @@ import { useKeyboardActionHandler } from "@/hooks/use-keyboard-action-handler";
 import type { KeyboardActionId } from "@/keyboard/keyboard-action-dispatcher";
 import { useFormPreferences } from "@/hooks/use-form-preferences";
 import { useShortcutKeys } from "@/hooks/use-shortcut-keys";
-import { getForgePresentation } from "@/git/forge";
 import type { CreateAgentInitialValues } from "@/hooks/use-agent-form-state";
 import { generateMessageId } from "@/types/stream";
 import { toErrorMessage } from "@/utils/error-messages";
@@ -90,12 +89,14 @@ import {
   remapDraftCwdToWorkspace,
 } from "./new-workspace-fork-context";
 import {
-  branchPickerOptionId,
+  buildPickerOptionData,
-  buildBranchPickerItems,
+  defaultBasePickerItem,
-  resolveCheckoutRequest,
+  pickerItemLabel,
+  pickerItemToCheckoutRequest,
   type BranchPickerDetail,
   type PickerCheckoutRequest,
   type PickerItem,
+  type PickerOptionData,
 } from "./new-workspace-picker-item";
 import {
   clearPickerPrAttachmentForTargetChange,
@@ -169,12 +170,6 @@ interface NewWorkspaceScreenProps {
   draftId?: string;
 }
 
-interface PickerOptionData {
-  options: ComboboxOptionType[];
-  itemById: Map<string, PickerItem>;
-}
-
-const PR_OPTION_PREFIX = "github-pr:";
 const PROJECT_ICON_FALLBACK_FONT_SIZE = 10;
 // Stable reference so the keyboard-action handler doesn't re-register each render.
 const PROJECT_PICK_ACTIONS: readonly KeyboardActionId[] = ["workspace.project.pick"];
@@ -475,10 +470,6 @@ function ProjectOptionItem({
   );
 }
 
-function prOptionId(number: number): string {
-  return `${PR_OPTION_PREFIX}${number}`;
-}
-
 function NewWorkspacePickerOption({
   option,
   selected,
@@ -590,57 +581,10 @@ function AddProjectPickerAction({ onPress }: { onPress: () => void }) {
   );
 }
 
-function formatPrLabel(item: Pick<ForgeSearchItem, "forge" | "number" | "title">): string {
-  const presentation = getForgePresentation(item.forge ?? "github");
-  return `${presentation.numberPrefix}${item.number} ${item.title}`;
-}
-
-function pickerItemLabel(item: PickerItem): string {
-  return item.kind === "branch" ? item.name : formatPrLabel(item.item);
-}
-
-function pickerItemTriggerLabel(item: PickerItem): string {
-  return item.kind === "branch" ? item.name : formatPrLabel(item.item);
-}
-
 function newWorkspaceHostOptionTestID(serverId: string): string {
   return `new-workspace-host-picker-option-${serverId}`;
 }
 
-function computePickerOptionData(
-  branchDetails: readonly BranchPickerDetail[],
-  prItems: ReadonlyArray<ForgeSearchItem>,
-): PickerOptionData {
-  const idMap = new Map<string, PickerItem>();
-
-  interface TimedOption {
-    option: ComboboxOptionType;
-    timestamp: number;
-  }
-  const timedOptions: TimedOption[] = [];
-
-  for (const branch of buildBranchPickerItems(branchDetails)) {
-    if (branch.kind !== "branch") continue;
-    const id = branchPickerOptionId(branch.refName);
-    const option = { id, label: branch.name };
-    idMap.set(id, branch);
-    timedOptions.push({ option, timestamp: branch.committerDate ?? 0 });
-  }
-
-  for (const pr of prItems) {
-    if (!pr.headRefName) continue;
-    const id = prOptionId(pr.number);
-    const option = { id, label: formatPrLabel(pr) };
-    idMap.set(id, { kind: "github-pr", item: pr });
-    const updatedAtMs = pr.updatedAt ? Date.parse(pr.updatedAt) : 0;
-    const timestamp = Number.isNaN(updatedAtMs) ? 0 : Math.floor(updatedAtMs / 1000);
-    timedOptions.push({ option, timestamp });
-  }
-
-  timedOptions.sort((a, b) => b.timestamp - a.timestamp);
-  return { options: timedOptions.map((t) => t.option), itemById: idMap };
-}
-
 function IsolationPickerTrigger({
   pickerAnchorRef,
   onPress,
@@ -1655,7 +1599,6 @@ export function NewWorkspaceScreen({
     cwd: selectedSourceDirectory ?? "",
   });
 
-  const currentBranch = checkoutStatus?.currentBranch ?? null;
   const worktreeSupport = selectedProject
     ? getWorktreeSupportForHostProject({ project: selectedProject, serverId: selectedServerId })
     : "unsupported";
@@ -1709,25 +1652,23 @@ export function NewWorkspaceScreen({
     return githubPrSearchQuery.data?.items ?? [];
   }, [forgeSearchAuthenticated, githubPrSearchQuery.data?.items]);
 
-  const { options, itemById }: PickerOptionData = useMemo(
+  const baseItem = useMemo(
-    () => computePickerOptionData(branchDetails, prItems),
+    () => selectedItem ?? (checkoutStatus ? defaultBasePickerItem(checkoutStatus) : null),
-    [branchDetails, prItems],
+    [checkoutStatus, selectedItem],
+  );
+  const { options, itemById, selectedOptionId }: PickerOptionData = useMemo(
+    () =>
+      buildPickerOptionData({
+        branchDetails,
+        prItems,
+        baseItem,
+      }),
+    [baseItem, branchDetails, prItems],
   );
   const triggerLabel = useMemo(() => {
-    if (selectedItem) return pickerItemTriggerLabel(selectedItem);
+    const displayItem = itemById.get(selectedOptionId);
-    return currentBranch ?? "main";
+    return displayItem ? pickerItemLabel(displayItem) : "main";
-  }, [currentBranch, selectedItem]);
+  }, [itemById, selectedOptionId]);
-
-  const selectedOptionId = useMemo(() => {
-    if (!selectedItem) {
-      if (!currentBranch) return "";
-      const exactLocalId = branchPickerOptionId(`refs/heads/${currentBranch}`);
-      return itemById.has(exactLocalId) ? exactLocalId : branchPickerOptionId(currentBranch);
-    }
-    return selectedItem.kind === "branch"
-      ? branchPickerOptionId(selectedItem.refName)
-      : prOptionId(selectedItem.item.number);
-  }, [currentBranch, itemById, selectedItem]);
   const selectPickerItem = useCallback(
     (item: PickerItem) => {
       const nextAttachments = syncPickerPrAttachment({
@@ -1929,15 +1870,17 @@ export function NewWorkspaceScreen({
       }
       const connectedClient = withConnectedClient();
       const createsWorktree = !supportsWorkspaceMultiplicity || effectiveIsolation === "worktree";
-      const checkoutRequest = createsWorktree
+      const checkoutStatusForCreate = createsWorktree
-        ? resolveCheckoutRequest(
+        ? await ensureCheckoutStatus({
-            selectedItem,
+            queryClient,
-            await ensureCheckoutStatus({
+            client: connectedClient,
-              queryClient,
+            serverId: selectedServerId,
-              client: connectedClient,
+            cwd: selectedSourceDirectory,
-              serverId: selectedServerId,
+          })
-              cwd: selectedSourceDirectory,
+        : null;
-            }),
+      const checkoutRequest = checkoutStatusForCreate
+        ? pickerItemToCheckoutRequest(
+            selectedItem ?? defaultBasePickerItem(checkoutStatusForCreate),
           )
         : undefined;
       const normalizedWorkspace = supportsWorkspaceMultiplicity

packages/protocol/src/messages.ts

@@ -4060,6 +4060,13 @@ const CheckoutStatusCommonSchema = z.object({
   cwd: z.string(),
   error: CheckoutErrorSchema.nullable(),
   requestId: z.string(),
+  // The full ref currentBranch tracks, as git resolves `<branch>@{upstream}`:
+  // "refs/remotes/origin/main", "refs/remotes/upstream/main" on a fork, or a
+  // "refs/heads/..." ref for a branch tracking a local branch. Null when there is no
+  // upstream. Clients use it verbatim — the remote is not necessarily origin and the
+  // upstream branch name is not necessarily currentBranch, so composing one is wrong.
+  // aheadOfOrigin/behindOfOrigin are measured against exactly this ref.
+  upstreamRef: z.string().nullable().optional(),
 });
 
 const CheckoutStatusNotGitSchema = CheckoutStatusCommonSchema.extend({

packages/server/src/server/checkout/status-projection.ts

@@ -33,6 +33,7 @@ export function buildCheckoutStatusPayloadFromSnapshot({
       isDirty: null,
       baseRef: null,
       aheadBehind: null,
+      upstreamRef: null,
       aheadOfOrigin: null,
       behindOfOrigin: null,
       hasRemote: false,
@@ -61,6 +62,7 @@ export function buildCheckoutStatusPayloadFromSnapshot({
       isDirty: snapshot.git.isDirty,
       baseRef: snapshot.git.baseRef,
       aheadBehind: snapshot.git.aheadBehind ?? null,
+      upstreamRef: snapshot.git.upstreamRef ?? null,
       aheadOfOrigin: snapshot.git.aheadOfOrigin ?? null,
       behindOfOrigin: snapshot.git.behindOfOrigin ?? null,
       hasRemote: snapshot.git.hasRemote,
@@ -80,6 +82,7 @@ export function buildCheckoutStatusPayloadFromSnapshot({
     isDirty: snapshot.git.isDirty,
     baseRef: snapshot.git.baseRef ?? null,
     aheadBehind: snapshot.git.aheadBehind ?? null,
+    upstreamRef: snapshot.git.upstreamRef ?? null,
     aheadOfOrigin: snapshot.git.aheadOfOrigin ?? null,
     behindOfOrigin: snapshot.git.behindOfOrigin ?? null,
     hasRemote: snapshot.git.hasRemote,

packages/server/src/server/session.test.ts

@@ -3373,6 +3373,7 @@ describe("session checkout status handling", () => {
         aheadBehind: { ahead: 2, behind: 1 },
         aheadOfOrigin: 2,
         behindOfOrigin: 1,
+        upstreamRef: null,
         hasRemote: true,
         remoteUrl: "https://github.com/getpaseo/paseo.git",
         isPaseoOwnedWorktree: false,

packages/server/src/server/websocket-server.ts

@@ -178,6 +178,7 @@ function createFallbackWorkspaceGitSnapshot(cwd: string): WorkspaceGitRuntimeSna
       isDirty: null,
       baseRef: null,
       aheadBehind: null,
+      upstreamRef: null,
       aheadOfOrigin: null,
       behindOfOrigin: null,
       hasRemote: false,

packages/server/src/server/workspace-git-service.ts

@@ -80,6 +80,7 @@ export interface WorkspaceGitRuntimeSnapshot {
     isDirty: boolean | null;
     baseRef: string | null;
     aheadBehind: { ahead: number; behind: number } | null;
+    upstreamRef: string | null;
     aheadOfOrigin: number | null;
     behindOfOrigin: number | null;
     hasRemote: boolean;
@@ -2182,6 +2183,7 @@ export class WorkspaceGitServiceImpl implements WorkspaceGitService {
         : (target.latestGit?.isDirty ?? checkoutStatus.isDirty),
       baseRef: checkoutStatus.baseRef,
       aheadBehind: checkoutStatus.aheadBehind,
+      upstreamRef: checkoutStatus.upstreamRef,
       aheadOfOrigin: checkoutStatus.aheadOfOrigin,
       behindOfOrigin: checkoutStatus.behindOfOrigin,
       hasRemote: checkoutStatus.hasRemote,
@@ -2598,6 +2600,7 @@ function buildNotGitSnapshot(cwd: string): WorkspaceGitRuntimeSnapshot {
       isDirty: null,
       baseRef: null,
       aheadBehind: null,
+      upstreamRef: null,
       aheadOfOrigin: null,
       behindOfOrigin: null,
       hasRemote: false,

packages/server/src/utils/checkout-git.test.ts

@@ -737,29 +737,107 @@ const x = 1;
     execFileSync("git", ["push"], { cwd: cloneDir });
     execFileSync("git", ["fetch", "origin"], { cwd: repoDir });
 
-    const facts = await getCheckoutSnapshotFacts(repoDir);
     startGitCommandMetrics();
+    const facts = await getCheckoutSnapshotFacts(repoDir);
     const divergedStatus = await getCheckoutStatus(repoDir, { facts });
     const metrics = stopGitCommandMetrics();
     const upstreamCountCommands = metrics.commands.filter(
-      (command) => command.args[0] === "rev-list" && command.args.join(" ").includes("main"),
+      (command) =>
+        command.args[0] === "for-each-ref" && command.args.join(" ").includes("%(upstream)"),
     );
 
     expect(divergedStatus.isGit).toBe(true);
     if (!divergedStatus.isGit) {
       return;
     }
+    expect(divergedStatus.upstreamRef).toBe("refs/remotes/origin/main");
     expect(divergedStatus.aheadOfOrigin).toBe(3);
     expect(divergedStatus.behindOfOrigin).toBe(2);
     expect(upstreamCountCommands).toHaveLength(1);
     expect(upstreamCountCommands[0]?.args).toEqual([
-      "rev-list",
+      "for-each-ref",
-      "--left-right",
+      "--format=%(upstream)%00%(upstream:track,nobracket)",
-      "--count",
+      "refs/heads/main",
-      "main...origin/main",
     ]);
   });
 
+  it("reports the fork remote, not origin, when the branch tracks a second remote", async () => {
+    setupRemoteTrackingMain(repoDir, tempDir);
+    const forkDir = join(tempDir, "fork.git");
+    execFileSync("git", ["init", "--bare", "-b", "main", forkDir]);
+    execFileSync("git", ["remote", "add", "upstream", forkDir], { cwd: repoDir });
+    execFileSync("git", ["push", "-u", "upstream", "main"], { cwd: repoDir });
+
+    const status = await getCheckoutStatus(repoDir);
+    expect(status.isGit).toBe(true);
+    if (!status.isGit) {
+      return;
+    }
+    expect(status.upstreamRef).toBe("refs/remotes/upstream/main");
+  });
+
+  it("reports the upstream branch name when it differs from the local branch name", async () => {
+    setupRemoteTrackingMain(repoDir, tempDir);
+    execFileSync("git", ["checkout", "-b", "feature"], { cwd: repoDir });
+    commitFile(repoDir, "feature.txt", "feature\n", "feature commit");
+    execFileSync("git", ["push", "-u", "origin", "HEAD:other-name"], { cwd: repoDir });
+
+    const status = await getCheckoutStatus(repoDir);
+    expect(status.isGit).toBe(true);
+    if (!status.isGit) {
+      return;
+    }
+    expect(status.upstreamRef).toBe("refs/remotes/origin/other-name");
+  });
+
+  it("reports the upstream when the repo's only remote is not origin", async () => {
+    const forkDir = join(tempDir, "fork.git");
+    execFileSync("git", ["init", "--bare", "-b", "main", forkDir]);
+    execFileSync("git", ["remote", "add", "upstream", forkDir], { cwd: repoDir });
+    execFileSync("git", ["push", "-u", "upstream", "main"], { cwd: repoDir });
+
+    const status = await getCheckoutStatus(repoDir);
+    expect(status.isGit).toBe(true);
+    if (!status.isGit) {
+      return;
+    }
+    expect(status.upstreamRef).toBe("refs/remotes/upstream/main");
+    expect(status.aheadOfOrigin).toBe(0);
+  });
+
+  // A legal local branch named "origin/main" shadows the short form "origin/main" in git's
+  // ref resolution. The counts and the reported ref have to describe the same commit.
+  it("is not fooled by a local branch named like the remote-tracking ref", async () => {
+    setupRemoteTrackingMain(repoDir, tempDir);
+    commitFile(repoDir, "shadow.txt", "shadow\n", "shadow commit");
+    // Pointed at HEAD, so comparing against the shadow reports 0 ahead while the real
+    // remote-tracking ref reports 1.
+    execFileSync("git", ["branch", "origin/main", "main"], { cwd: repoDir });
+
+    const status = await getCheckoutStatus(repoDir);
+    expect(status.isGit).toBe(true);
+    if (!status.isGit) {
+      return;
+    }
+    expect(status.upstreamRef).toBe("refs/remotes/origin/main");
+    expect(status.aheadOfOrigin).toBe(1);
+    expect(status.behindOfOrigin).toBe(0);
+  });
+
+  it("reports no upstream ref for a branch that was never pushed", async () => {
+    setupRemoteTrackingMain(repoDir, tempDir);
+    execFileSync("git", ["checkout", "-b", "local-only"], { cwd: repoDir });
+    commitFile(repoDir, "local-only.txt", "local\n", "local commit");
+
+    const status = await getCheckoutStatus(repoDir);
+    expect(status.isGit).toBe(true);
+    if (!status.isGit) {
+      return;
+    }
+    expect(status.upstreamRef).toBeNull();
+    expect(status.aheadOfOrigin).toBeNull();
+  });
+
   it("reports a PR worktree as not ahead when its branch is pushed to the configured PR remote", async () => {
     setupRemoteTrackingMain(repoDir, tempDir);
     const prRemoteDir = join(tempDir, "pr-remote.git");
@@ -3396,7 +3474,7 @@ const x = 1;
 
     await expect(
       getCheckoutDiff(worktree.worktreePath, { mode: "base", baseRef: "other" }, { paseoHome }),
-    ).rejects.toThrow("Base ref mismatch: stored main, requested other");
+    ).rejects.toThrow("Base ref mismatch: stored refs/heads/main, requested other");
   });
 
   it("excludes dirty working tree changes from Paseo worktree base diffs", async () => {

packages/server/src/utils/checkout-git.ts

@@ -30,6 +30,7 @@ import { parseGitRevParsePath, resolveGitRevParsePath } from "./git-rev-parse-pa
 import { runGitCommand } from "./run-git-command.js";
 import { isPaseoOwnedWorktreeCwd, resolvePaseoWorktreesBaseRoot } from "./worktree.js";
 import {
+  branchNameFromRef,
   getPaseoWorktreeChangeRequestHintForBranch,
   type PaseoWorktreeMetadata,
   readPaseoWorktreeMetadata,
@@ -786,6 +787,10 @@ export interface CheckoutStatusGitNonPaseo {
   isDirty: boolean;
   baseRef: string | null;
   aheadBehind: AheadBehind | null;
+  // Remote-tracking ref for currentBranch, e.g. "refs/remotes/origin/main". Null when the
+  // branch has no upstream or git could not resolve it. aheadOfOrigin/behindOfOrigin are
+  // measured against exactly this ref.
+  upstreamRef: string | null;
   aheadOfOrigin: number | null;
   behindOfOrigin: number | null;
   hasRemote: boolean;
@@ -801,6 +806,7 @@ export interface CheckoutStatusGitPaseo {
   isDirty: boolean;
   baseRef: string;
   aheadBehind: AheadBehind | null;
+  upstreamRef: string | null;
   aheadOfOrigin: number | null;
   behindOfOrigin: number | null;
   hasRemote: boolean;
@@ -859,6 +865,7 @@ export type CheckoutSnapshotFacts =
       comparisonBaseRef: string | null;
       branchRemoteName: string | null;
       branchMergeRef: string | null;
+      upstreamStatus: UpstreamStatus | null;
       pullRequestLookupTarget: PullRequestStatusLookupTarget | null;
     };
 
@@ -1153,8 +1160,14 @@ async function getPaseoWorktreeForCwd(
   };
 }
 
+// Worktrees created before baseRef existed only stored the stripped name; it resolves
+// local-first, which is the base they were actually cut from.
+function storedBaseRefFromMetadata(metadata: PaseoWorktreeMetadata | null): string | null {
+  return metadata?.baseRef ?? metadata?.baseRefName ?? null;
+}
+
 function readPaseoWorktreeBaseRef(worktreeRoot: string): string | null {
-  return readPaseoWorktreeMetadata(worktreeRoot)?.baseRefName ?? null;
+  return storedBaseRefFromMetadata(readPaseoWorktreeMetadata(worktreeRoot));
 }
 
 async function getStoredBaseRefForCwd(
@@ -1205,12 +1218,37 @@ async function resolveBaseRefForCwd(
   };
 }
 
+// The worktree stores the exact ref it was cut from ("refs/remotes/upstream/main") while
+// callers still send its display name ("main"). A different qualified ref retains its own
+// identity even when it has the same branch name.
+function isSameBaseRef(stored: string, requested: string): boolean {
+  return stored === requested || branchNameFromRef(stored) === requested;
+}
+
 // Names both refs rather than labelling either one correct: a caller's ref can be stale, but the
 // stored ref can equally be wrong, so the message states the two facts and leaves the diagnosis open.
 function baseRefMismatchError(refs: { stored: string; requested: string }): Error {
   return new Error(`Base ref mismatch: stored ${refs.stored}, requested ${refs.requested}`);
 }
 
+function resolveOperationBaseRef(input: {
+  storedBaseRef: string | null;
+  resolvedBaseRef: string | null;
+  requestedBaseRef?: string;
+}): string | null {
+  if (
+    input.storedBaseRef &&
+    input.requestedBaseRef &&
+    !isSameBaseRef(input.storedBaseRef, input.requestedBaseRef)
+  ) {
+    throw baseRefMismatchError({
+      stored: input.storedBaseRef,
+      requested: input.requestedBaseRef,
+    });
+  }
+  return input.storedBaseRef ?? input.requestedBaseRef ?? input.resolvedBaseRef;
+}
+
 async function isWorkingTreeDirty(cwd: string, context?: CheckoutContext): Promise<boolean> {
   const { stdout } = await runGitCommand(["status", "--porcelain"], {
     cwd,
@@ -1450,29 +1488,25 @@ async function resolveBaseRef(repoRoot: string): Promise<string | null> {
   return resolveRepositoryDefaultBranch(repoRoot);
 }
 
-function normalizeLocalBranchRefName(input: string): string {
-  if (input.startsWith("refs/remotes/origin/")) {
-    return input.slice("refs/remotes/origin/".length);
-  }
-  if (input.startsWith("refs/heads/")) {
-    return input.slice("refs/heads/".length);
-  }
-  if (input.startsWith("origin/")) {
-    return input.slice("origin/".length);
-  }
-  return input;
-}
-
 interface ComparisonBaseRefName {
   localName: string;
   originRef: string;
 }
 
 function normalizeComparisonBaseRefName(input: string): ComparisonBaseRefName {
-  const localName = normalizeLocalBranchRefName(input);
+  const localName = branchNameFromRef(input);
   return { localName, originRef: `origin/${localName}` };
 }
 
+function resolveMergeTargetBranch(baseRef: string): string {
+  const remotePrefix = "refs/remotes/";
+  const originPrefix = `${remotePrefix}origin/`;
+  if (baseRef.startsWith(remotePrefix) && !baseRef.startsWith(originPrefix)) {
+    throw new Error(`No local merge target is recorded for base ref ${baseRef}`);
+  }
+  return branchNameFromRef(baseRef);
+}
+
 async function doesGitRefExist(
   cwd: string,
   fullRef: string,
@@ -1487,11 +1521,23 @@ async function doesGitRefExist(
   return result.exitCode === 0;
 }
 
+function isQualifiedBranchRef(ref: string): boolean {
+  return ref.startsWith("refs/heads/") || ref.startsWith("refs/remotes/");
+}
+
 async function resolveBestComparisonBaseRef(
   cwd: string,
   baseRef: string,
   context?: CheckoutContext,
 ): Promise<string> {
+  // A fully qualified branch ref names the exact commit stream to compare against. Bare names
+  // keep going through the local-vs-origin heuristic below for legacy worktree metadata.
+  if (isQualifiedBranchRef(baseRef)) {
+    if (await doesGitRefExist(cwd, baseRef, context)) {
+      return baseRef;
+    }
+    throw new Error(`Base ref not found: ${baseRef}`);
+  }
   const normalized = normalizeComparisonBaseRefName(baseRef);
   const [hasLocal, hasOrigin] = await Promise.all([
     doesGitRefExist(cwd, `refs/heads/${normalized.localName}`, context),
@@ -1512,7 +1558,14 @@ async function resolveBestComparisonBaseRef(
   throw new Error(`Base branch not found locally or on origin: ${refName}`);
 }
 
-async function resolveMostAheadBaseRef(cwd: string, normalizedBaseRef: string): Promise<string> {
+async function resolveMostAheadBaseRef(cwd: string, baseRef: string): Promise<string> {
+  if (isQualifiedBranchRef(baseRef)) {
+    if (await doesGitRefExist(cwd, baseRef)) {
+      return baseRef;
+    }
+    throw new Error(`Base ref not found: ${baseRef}`);
+  }
+  const normalizedBaseRef = branchNameFromRef(baseRef);
   const [hasLocal, hasOrigin] = await Promise.all([
     doesGitRefExist(cwd, `refs/heads/${normalizedBaseRef}`),
     doesGitRefExist(cwd, `refs/remotes/origin/${normalizedBaseRef}`),
@@ -1551,7 +1604,7 @@ async function getAheadBehind(
   currentBranch: string,
   context?: CheckoutContext,
 ): Promise<AheadBehind | null> {
-  const normalizedBaseRef = normalizeLocalBranchRefName(baseRef);
+  const normalizedBaseRef = branchNameFromRef(baseRef);
   if (!normalizedBaseRef || !currentBranch || normalizedBaseRef === currentBranch) {
     return null;
   }
@@ -1575,48 +1628,32 @@ async function getAheadBehind(
   return { ahead, behind };
 }
 
-async function getConfiguredUpstreamRef(
+interface UpstreamStatus {
-  cwd: string,
+  ref: string;
-  currentBranch: string,
+  aheadBehind: AheadBehind;
-  context?: CheckoutContext,
-): Promise<string | null> {
-  const remoteName =
-    context?.facts?.isGit && context.facts.currentBranch === currentBranch
-      ? context.facts.branchRemoteName
-      : await getGitConfigValue(cwd, `branch.${currentBranch}.remote`, context);
-  if (!remoteName) {
-    return null;
-  }
-
-  const mergeRef =
-    context?.facts?.isGit && context.facts.currentBranch === currentBranch
-      ? context.facts.branchMergeRef
-      : await getGitConfigValue(cwd, `branch.${currentBranch}.merge`, context);
-  const upstreamBranch = parseBranchMergeHeadRef(mergeRef);
-  return upstreamBranch ? `${remoteName}/${upstreamBranch}` : null;
 }
 
-async function getOriginAheadBehind(
+async function getUpstreamStatus(
   cwd: string,
   currentBranch: string,
   context?: CheckoutContext,
-): Promise<AheadBehind | null> {
+): Promise<UpstreamStatus | null> {
-  if (!currentBranch) {
-    return null;
-  }
-  const upstreamRef = await getConfiguredUpstreamRef(cwd, currentBranch, context);
-  if (!upstreamRef) {
-    return null;
-  }
   try {
     const { stdout } = await runGitCommand(
-      ["rev-list", "--left-right", "--count", `${currentBranch}...${upstreamRef}`],
+      [
+        "for-each-ref",
+        "--format=%(upstream)%00%(upstream:track,nobracket)",
+        `refs/heads/${currentBranch}`,
+      ],
       { cwd, envOverlay: READ_ONLY_GIT_ENV, logger: context?.logger },
     );
-    const [aheadRaw, behindRaw] = stdout.trim().split(/\s+/);
+    const [ref = "", track = ""] = stdout.trim().split("\0", 2);
-    const ahead = Number.parseInt(aheadRaw ?? "", 10);
+    if (!ref || track === "gone") {
-    const behind = Number.parseInt(behindRaw ?? "", 10);
+      return null;
-    return Number.isNaN(ahead) || Number.isNaN(behind) ? null : { ahead, behind };
+    }
+    const ahead = Number.parseInt(track.match(/ahead (\d+)/)?.[1] ?? "0", 10);
+    const behind = Number.parseInt(track.match(/behind (\d+)/)?.[1] ?? "0", 10);
+    return { ref, aheadBehind: { ahead, behind } };
   } catch {
     return null;
   }
@@ -1674,9 +1711,7 @@ function buildPullRequestLookupTargetFromBranchConfig(
   const originRepo = parseRepositoryIdentityFromRemote(input.originRemoteUrl);
   const isSameRepo = areSameGitHubRepository(remoteRepo, originRepo);
   const headRepositoryOwner = remoteRepo && !isSameRepo ? remoteRepo.split("/")[0] : null;
-  const normalizedBaseRef = input.resolvedBaseRef
+  const normalizedBaseRef = input.resolvedBaseRef ? branchNameFromRef(input.resolvedBaseRef) : null;
-    ? normalizeLocalBranchRefName(input.resolvedBaseRef)
-    : null;
   if (
     trackedHeadRef === normalizedBaseRef &&
     !doesLocalBranchNameIdentifyTrackedHead(
@@ -1740,9 +1775,7 @@ function buildPullRequestLookupTargetFromPushConfig(
     : null;
   const isSameRepo = areSameGitHubRepository(remoteRepo, originRepo);
   const headRepositoryOwner = remoteRepo && !isSameRepo ? remoteRepo.split("/")[0] : null;
-  const normalizedBaseRef = input.resolvedBaseRef
+  const normalizedBaseRef = input.resolvedBaseRef ? branchNameFromRef(input.resolvedBaseRef) : null;
-    ? normalizeLocalBranchRefName(input.resolvedBaseRef)
-    : null;
   if (pushedHeadRef === normalizedBaseRef && !headRepositoryOwner) {
     return null;
   }
@@ -1855,7 +1888,7 @@ export async function getCheckoutSnapshotFacts(
   const paseoWorktreeMetadata = inspected.paseoWorktree.isPaseoOwnedWorktree
     ? readPaseoWorktreeMetadata(inspected.paseoWorktree.worktreeRoot)
     : null;
-  const storedBaseRef = paseoWorktreeMetadata?.baseRefName ?? null;
+  const storedBaseRef = storedBaseRefFromMetadata(paseoWorktreeMetadata);
   const resolvedBaseRef = storedBaseRef ?? (await resolveBaseRef(cwd));
   const mainRepoRoot = await getMainRepoRootFromCommonDir(
     cwd,
@@ -1866,7 +1899,7 @@ export async function getCheckoutSnapshotFacts(
   if (
     resolvedBaseRef &&
     inspected.currentBranch &&
-    normalizeLocalBranchRefName(resolvedBaseRef) !== inspected.currentBranch
+    branchNameFromRef(resolvedBaseRef) !== inspected.currentBranch
   ) {
     comparisonBaseRef = await resolveBestComparisonBaseRef(cwd, resolvedBaseRef, context).catch(
       () => null,
@@ -1876,6 +1909,9 @@ export async function getCheckoutSnapshotFacts(
   let branchRemoteName: string | null = null;
   let branchMergeRef: string | null = null;
   let branchRemoteUrl: string | null = null;
+  const upstreamStatusPromise = inspected.currentBranch
+    ? getUpstreamStatus(cwd, inspected.currentBranch, context)
+    : Promise.resolve(null);
   if (inspected.currentBranch) {
     branchRemoteName = await getGitConfigValue(
       cwd,
@@ -1919,6 +1955,7 @@ export async function getCheckoutSnapshotFacts(
     pullRequestLookupTarget,
     context,
   );
+  const upstreamStatus = await upstreamStatusPromise;
 
   return {
     isGit: true,
@@ -1934,6 +1971,7 @@ export async function getCheckoutSnapshotFacts(
     comparisonBaseRef,
     branchRemoteName,
     branchMergeRef,
+    upstreamStatus,
     pullRequestLookupTarget,
   };
 }
@@ -2097,16 +2135,18 @@ export async function getCheckoutStatus(
   const baseRef = facts.resolvedBaseRef;
   const mainRepoRoot = facts.mainRepoRoot;
   const factsContext = { ...context, facts };
-  const [aheadBehind, originAheadBehind] = await Promise.all([
+  const aheadBehind =
     baseRef && currentBranch
-      ? getAheadBehind(cwd, baseRef, currentBranch, factsContext)
+      ? await getAheadBehind(cwd, baseRef, currentBranch, factsContext)
-      : Promise.resolve(null),
+      : null;
-    hasRemote && currentBranch
+  const upstreamStatus = facts.upstreamStatus;
-      ? getOriginAheadBehind(cwd, currentBranch, factsContext)
+  // The wire carries the display name: clients label the base with it and send it back to
-      : Promise.resolve(null),
+  // request diffs and merges. The exact ref stays in worktree.json and in facts, where the
-  ]);
+  // comparisons and actions read it.
-  const aheadOfOrigin = originAheadBehind?.ahead ?? null;
+  const displayBaseRef = baseRef ? branchNameFromRef(baseRef) : null;
-  const behindOfOrigin = originAheadBehind?.behind ?? null;
+  const upstreamRef = upstreamStatus?.ref ?? null;
+  const aheadOfOrigin = upstreamStatus?.aheadBehind.ahead ?? null;
+  const behindOfOrigin = upstreamStatus?.aheadBehind.behind ?? null;
 
   if (paseoWorktree.isPaseoOwnedWorktree && baseRef) {
     return {
@@ -2115,8 +2155,9 @@ export async function getCheckoutStatus(
       mainRepoRoot: mainRepoRoot ?? worktreeRoot,
       currentBranch,
       isDirty,
-      baseRef,
+      baseRef: displayBaseRef ?? baseRef,
       aheadBehind,
+      upstreamRef,
       aheadOfOrigin,
       behindOfOrigin,
       hasRemote,
@@ -2132,8 +2173,9 @@ export async function getCheckoutStatus(
       mainRepoRoot && resolve(mainRepoRoot) !== resolve(worktreeRoot) ? mainRepoRoot : null,
     currentBranch,
     isDirty,
-    baseRef,
+    baseRef: displayBaseRef,
     aheadBehind,
+    upstreamRef,
     aheadOfOrigin,
     behindOfOrigin,
     hasRemote,
@@ -2345,11 +2387,18 @@ async function tryResolveCheckoutCommitsBaseRef(
   if (!baseRef) {
     return null;
   }
-  const normalizedBaseRef = normalizeLocalBranchRefName(baseRef);
+  const normalizedBaseRef = branchNameFromRef(baseRef);
   if (!normalizedBaseRef || normalizedBaseRef === currentBranch) {
     return null;
   }
-  return resolveMostAheadBaseRef(cwd, normalizedBaseRef).catch(() => null);
+  try {
+    return await resolveMostAheadBaseRef(cwd, baseRef);
+  } catch (error) {
+    if (isQualifiedBranchRef(baseRef)) {
+      throw error;
+    }
+    return null;
+  }
 }
 
 export async function listCheckoutCommits({
@@ -2365,7 +2414,7 @@ export async function listCheckoutCommits({
   }
 
   const { resolvedBaseRef } = await resolveBaseRefForCwd(cwd, context);
-  const normalizedBaseRef = resolvedBaseRef ? normalizeLocalBranchRefName(resolvedBaseRef) : null;
+  const normalizedBaseRef = resolvedBaseRef ? branchNameFromRef(resolvedBaseRef) : null;
   let comparisonBaseRef = await tryResolveCheckoutCommitsBaseRef(
     cwd,
     resolvedBaseRef,
@@ -2991,13 +3040,14 @@ async function resolveCheckoutDiffRefs(
     return { baseRef: "HEAD", includeUntracked: true };
   }
   const { storedBaseRef, resolvedBaseRef } = await resolveBaseRefForCwd(cwd, context);
-  const baseRef = compare.baseRef ?? resolvedBaseRef;
+  const baseRef = resolveOperationBaseRef({
+    storedBaseRef,
+    resolvedBaseRef,
+    requestedBaseRef: compare.baseRef,
+  });
   if (!baseRef) {
     return null;
   }
-  if (storedBaseRef && compare.baseRef && compare.baseRef !== storedBaseRef) {
-    throw baseRefMismatchError({ stored: storedBaseRef, requested: compare.baseRef });
-  }
   const bestBaseRef = await resolveBestComparisonBaseRef(cwd, baseRef);
   return {
     baseRef: (await tryResolveMergeBase(cwd, bestBaseRef)) ?? bestBaseRef,
@@ -3209,18 +3259,18 @@ export async function mergeToBase(
   await requireGitRepo(cwd);
   const currentBranch = await getCurrentBranch(cwd);
   const { storedBaseRef, resolvedBaseRef } = await resolveBaseRefForCwd(cwd, context);
-  const baseRef = options.baseRef ?? resolvedBaseRef;
+  const baseRef = resolveOperationBaseRef({
+    storedBaseRef,
+    resolvedBaseRef,
+    requestedBaseRef: options.baseRef,
+  });
   if (!baseRef) {
     throw new Error("Unable to determine base branch for merge");
   }
-  if (storedBaseRef && options.baseRef && options.baseRef !== storedBaseRef) {
-    throw baseRefMismatchError({ stored: storedBaseRef, requested: options.baseRef });
-  }
   if (!currentBranch) {
     throw new Error("Unable to determine current branch for merge");
   }
-  let normalizedBaseRef = baseRef;
+  const normalizedBaseRef = resolveMergeTargetBranch(baseRef);
-  normalizedBaseRef = normalizeLocalBranchRefName(normalizedBaseRef);
   const currentWorktreeRoot = (await getWorktreeRoot(cwd, context)) ?? cwd;
   if (normalizedBaseRef === currentBranch) {
     return currentWorktreeRoot;
@@ -3285,13 +3335,14 @@ export async function mergeFromBase(
   }
 
   const { storedBaseRef, resolvedBaseRef } = await resolveBaseRefForCwd(cwd, context);
-  const baseRef = options.baseRef ?? resolvedBaseRef;
+  const baseRef = resolveOperationBaseRef({
+    storedBaseRef,
+    resolvedBaseRef,
+    requestedBaseRef: options.baseRef,
+  });
   if (!baseRef) {
     throw new Error("Unable to determine base branch for merge");
   }
-  if (storedBaseRef && options.baseRef && options.baseRef !== storedBaseRef) {
-    throw baseRefMismatchError({ stored: storedBaseRef, requested: options.baseRef });
-  }
 
   const requireCleanTarget = options.requireCleanTarget ?? true;
   if (requireCleanTarget) {
@@ -3304,8 +3355,7 @@ export async function mergeFromBase(
     }
   }
 
-  const normalizedBaseRef = normalizeLocalBranchRefName(baseRef);
+  const bestBaseRef = await resolveMostAheadBaseRef(cwd, baseRef);
-  const bestBaseRef = await resolveMostAheadBaseRef(cwd, normalizedBaseRef);
   if (bestBaseRef === currentBranch) {
     return;
   }
@@ -3619,17 +3669,18 @@ export async function createPullRequest(
 
   const head = options.head ?? (await getCurrentBranch(cwd));
   const { storedBaseRef, resolvedBaseRef } = await resolveBaseRefForCwd(cwd, context);
-  const base = options.base ?? resolvedBaseRef;
+  const base = resolveOperationBaseRef({
+    storedBaseRef,
+    resolvedBaseRef,
+    requestedBaseRef: options.base,
+  });
   if (!head) {
     throw new Error("Unable to determine head branch for PR");
   }
   if (!base) {
     throw new Error("Unable to determine base branch for PR");
   }
-  const normalizedBase = normalizeLocalBranchRefName(base);
+  const normalizedBase = branchNameFromRef(base);
-  if (storedBaseRef && options.base && options.base !== storedBaseRef) {
-    throw baseRefMismatchError({ stored: storedBaseRef, requested: options.base });
-  }
 
   // The push deliberately happens before the adapter resolves the target
   // repository: slug resolution is adapter-internal (e.g. `gh repo view`, which

packages/server/src/utils/worktree-metadata.ts

@@ -9,15 +9,20 @@ const ChangeRequestLookupTargetSchema = z.object({
   localBranchName: z.string().min(1).optional(),
 });
 
+// baseRefName is the display name; baseRef is the exact ref the worktree was cut from
+// ("refs/remotes/upstream/main"). baseRef is optional because worktrees written before it
+// existed only have the name — there are no migrations, so readers fall back.
 const PaseoWorktreeMetadataV1Schema = z.object({
   version: z.literal(1),
   baseRefName: z.string().min(1),
+  baseRef: z.string().min(1).optional(),
   changeRequestLookupTarget: ChangeRequestLookupTargetSchema.optional(),
 });
 
 const PaseoWorktreeMetadataV2Schema = z.object({
   version: z.literal(2),
   baseRefName: z.string().min(1),
+  baseRef: z.string().min(1).optional(),
   changeRequestLookupTarget: ChangeRequestLookupTargetSchema.optional(),
   firstAgentBranchAutoName: z
     .discriminatedUnion("status", [
@@ -133,44 +138,72 @@ export function getPaseoWorktreeMetadataPath(worktreeRoot: string): string {
   return join(gitDir, "paseo", "worktree.json");
 }
 
-export function normalizeBaseRefName(input: string): string {
+const REMOTE_TRACKING_PREFIX = "refs/remotes/";
-  const trimmed = input.trim();
+
-  if (!trimmed) {
+/**
-    throw new Error("Base branch is required");
+ * The human-readable branch name behind a ref. Display and legacy identity only — it cannot
-  }
+ * round-trip, so anything that has to resolve to a commit keeps the exact ref instead.
+ *
+ * refs/remotes/<remote>/<branch> works for any remote, not just origin. Git allows slashes in
+ * remote names, so refs/remotes/a/b/c is ambiguous and the first segment is read as the
+ * remote: slashes are everywhere in branch names and rare in remote names. A remote genuinely
+ * named "team/upstream" therefore displays as "upstream/main" rather than "main"; the exact
+ * ref is unaffected, which is why this is display-only.
+ */
+export function branchNameFromRef(ref: string): string {
+  const trimmed = ref.trim();
   if (trimmed.startsWith("refs/heads/")) {
     return trimmed.slice("refs/heads/".length);
   }
-  if (trimmed.startsWith("refs/remotes/origin/")) {
+  if (trimmed.startsWith(REMOTE_TRACKING_PREFIX)) {
-    return trimmed.slice("refs/remotes/origin/".length);
+    const remainder = trimmed.slice(REMOTE_TRACKING_PREFIX.length);
+    const separator = remainder.indexOf("/");
+    return separator === -1 ? remainder : remainder.slice(separator + 1);
   }
+  // Short form. It cannot be generalized to any remote the way the qualified form can:
+  // without the remote list, "feature/x" is indistinguishable from "<remote>/x".
   if (trimmed.startsWith("origin/")) {
     return trimmed.slice("origin/".length);
   }
   return trimmed;
 }
 
+export function normalizeBaseRefName(input: string): string {
+  const trimmed = input.trim();
+  if (!trimmed) {
+    throw new Error("Base branch is required");
+  }
+  return branchNameFromRef(trimmed);
+}
+
+function assertValidBaseRef(value: string): void {
+  if (value === "HEAD") {
+    throw new Error("Base branch cannot be HEAD");
+  }
+  if (value.includes("..") || value.includes("@{")) {
+    throw new Error(`Invalid base branch: ${value}`);
+  }
+}
+
 export function writePaseoWorktreeMetadata(
   worktreeRoot: string,
   options: {
     baseRefName: string;
+    baseRef?: string;
     changeRequestLookupTarget?: PaseoWorktreeChangeRequestHint;
   },
 ): void {
   const baseRefName = normalizeBaseRefName(options.baseRefName);
-  if (baseRefName === "HEAD") {
+  assertValidBaseRef(baseRefName);
-    throw new Error("Base branch cannot be HEAD");
+  const baseRef = options.baseRef?.trim();
-  }
+  if (baseRef) {
-  if (baseRefName.includes("..") || baseRefName.includes("@{")) {
+    assertValidBaseRef(baseRef);
-    throw new Error(`Invalid base branch: ${baseRefName}`);
-  }
-  if (!/^[0-9A-Za-z._/-]+$/.test(baseRefName)) {
-    throw new Error(`Invalid base branch: ${baseRefName}`);
   }
 
   const metadata: PaseoWorktreeMetadata = {
     version: 1,
     baseRefName,
+    ...(baseRef ? { baseRef } : {}),
     ...(options.changeRequestLookupTarget
       ? { changeRequestLookupTarget: options.changeRequestLookupTarget }
       : {}),
@@ -192,14 +225,8 @@ export function writePaseoWorktreeRuntimeMetadata(
   }
 
   const next: PaseoWorktreeMetadata = {
+    ...current,
     version: 2,
-    baseRefName: current.baseRefName,
-    ...(current.changeRequestLookupTarget
-      ? { changeRequestLookupTarget: current.changeRequestLookupTarget }
-      : {}),
-    ...(current.version === 2 && current.firstAgentBranchAutoName
-      ? { firstAgentBranchAutoName: current.firstAgentBranchAutoName }
-      : {}),
     runtime: {
       worktreePort: options.worktreePort,
     },
@@ -222,16 +249,12 @@ export function writePaseoWorktreeFirstAgentBranchAutoNameMetadata(
   }
 
   writePaseoWorktreeMetadataFile(worktreeRoot, {
+    ...current,
     version: 2,
-    baseRefName: current.baseRefName,
-    ...(current.changeRequestLookupTarget
-      ? { changeRequestLookupTarget: current.changeRequestLookupTarget }
-      : {}),
     firstAgentBranchAutoName: {
       status: "pending",
       placeholderBranchName,
     },
-    ...(current.version === 2 && current.runtime ? { runtime: current.runtime } : {}),
   });
 }
 
@@ -245,17 +268,12 @@ export function markPaseoWorktreeFirstAgentBranchAutoNameAttempted(
   }
 
   const next: PaseoWorktreeMetadata = {
-    version: 2,
+    ...current,
-    baseRefName: current.baseRefName,
-    ...(current.changeRequestLookupTarget
-      ? { changeRequestLookupTarget: current.changeRequestLookupTarget }
-      : {}),
     firstAgentBranchAutoName: {
       status: "attempted",
       placeholderBranchName: current.firstAgentBranchAutoName.placeholderBranchName,
       attemptedAt: options.attemptedAt ?? new Date().toISOString(),
     },
-    ...(current.runtime ? { runtime: current.runtime } : {}),
   };
   writePaseoWorktreeMetadataFile(worktreeRoot, next);
   return next;

packages/server/src/utils/worktree.posix.test.ts

@@ -23,6 +23,13 @@ import {
 } from "./worktree";
 import type { PaseoConfig } from "@getpaseo/protocol/paseo-config-schema";
 import { getPaseoWorktreeMetadataPath } from "./worktree-metadata.js";
+import {
+  getCheckoutDiff,
+  getCheckoutStatus,
+  listCheckoutCommits,
+  mergeFromBase,
+  mergeToBase,
+} from "./checkout-git.js";
 import { execFileSync } from "child_process";
 import { isPlatform } from "../test-utils/platform.js";
 import {
@@ -436,7 +443,7 @@ describe.skipIf(isPlatform("win32"))("worktree POSIX-only", () => {
       const localResult = await createLegacyWorktreeForTest({
         branchName: "prefer-local-feature",
         cwd: repoDir,
-        baseBranch: "main",
+        baseBranch: "refs/heads/main",
         worktreeSlug: "prefer-local-feature",
         runSetup: false,
         paseoHome,
@@ -451,6 +458,15 @@ describe.skipIf(isPlatform("win32"))("worktree POSIX-only", () => {
       });
 
       expect(readFileSync(join(localResult.worktreePath, "file.txt"), "utf8")).toBe("from-local\n");
+      const localStatus = await getCheckoutStatus(localResult.worktreePath, { paseoHome });
+      expect(localStatus.isGit).toBe(true);
+      if (!localStatus.isGit) {
+        return;
+      }
+      expect(localStatus.aheadBehind).toEqual({ ahead: 0, behind: 0 });
+      await expect(
+        getCheckoutDiff(localResult.worktreePath, { mode: "base", baseRef: "main" }, { paseoHome }),
+      ).resolves.toMatchObject({ diff: "" });
       expect(readFileSync(join(originResult.worktreePath, "file.txt"), "utf8")).toBe(
         "from-origin\n",
       );
@@ -459,6 +475,137 @@ describe.skipIf(isPlatform("win32"))("worktree POSIX-only", () => {
       ).toMatchObject({ baseRefName: "main" });
     });
 
+    it("records the branch name when the base is on a remote other than origin", async () => {
+      const forkDir = join(tempDir, "fork.git");
+      const forkCloneDir = join(tempDir, "fork-clone");
+      execFileSync("git", ["init", "--bare", forkDir]);
+      execFileSync("git", ["remote", "add", "upstream", forkDir], { cwd: repoDir });
+      execFileSync("git", ["push", "-u", "upstream", "main"], { cwd: repoDir });
+
+      execFileSync("git", ["clone", "--branch", "main", forkDir, forkCloneDir]);
+      execFileSync("git", ["config", "user.email", "test@test.com"], { cwd: forkCloneDir });
+      execFileSync("git", ["config", "user.name", "Test"], { cwd: forkCloneDir });
+      writeFileSync(join(forkCloneDir, "file.txt"), "from-upstream\n");
+      execFileSync("git", ["add", "file.txt"], { cwd: forkCloneDir });
+      execFileSync("git", ["-c", "commit.gpgsign=false", "commit", "-m", "advance upstream main"], {
+        cwd: forkCloneDir,
+      });
+      execFileSync("git", ["push", "origin", "main"], { cwd: forkCloneDir });
+      execFileSync("git", ["fetch", "upstream"], { cwd: repoDir });
+      const localMainHead = execFileSync("git", ["rev-parse", "refs/heads/main"], {
+        cwd: repoDir,
+      })
+        .toString()
+        .trim();
+
+      const result = await createLegacyWorktreeForTest({
+        branchName: "fork-base-feature",
+        cwd: repoDir,
+        baseBranch: "refs/remotes/upstream/main",
+        worktreeSlug: "fork-base-feature",
+        runSetup: false,
+        paseoHome,
+      });
+
+      expect(readFileSync(join(result.worktreePath, "file.txt"), "utf8")).toBe("from-upstream\n");
+      // The display name and the exact ref are both recorded. Only the ref can resolve back
+      // to the commit the worktree was cut from: "main" resolves local-first, which here is
+      // a different commit than the fork's upstream.
+      expect(
+        JSON.parse(readFileSync(getPaseoWorktreeMetadataPath(result.worktreePath), "utf8")),
+      ).toMatchObject({ baseRefName: "main", baseRef: "refs/remotes/upstream/main" });
+
+      // An untouched child must report no work of its own. Comparing against the wrong base
+      // shows the upstream-only commit as if the workspace had written it.
+      const status = await getCheckoutStatus(result.worktreePath, { paseoHome });
+      expect(status.isGit).toBe(true);
+      if (!status.isGit) {
+        return;
+      }
+      // The wire keeps the display name; the exact ref above is what the comparison used,
+      // which is why an untouched child reports no work of its own.
+      expect(status.baseRef).toBe("main");
+      expect(status.aheadBehind).toEqual({ ahead: 0, behind: 0 });
+      await expect(
+        getCheckoutDiff(
+          result.worktreePath,
+          { mode: "base", baseRef: "refs/remotes/origin/main" },
+          { paseoHome },
+        ),
+      ).rejects.toThrow(
+        "Base ref mismatch: stored refs/remotes/upstream/main, requested refs/remotes/origin/main",
+      );
+      expect(
+        await getCheckoutDiff(
+          result.worktreePath,
+          { mode: "base", baseRef: "main" },
+          { paseoHome },
+        ),
+      ).toMatchObject({ diff: "" });
+      const history = await listCheckoutCommits({
+        cwd: result.worktreePath,
+        context: { paseoHome },
+      });
+      expect(history.commits.every((commit) => commit.isOnBase)).toBe(true);
+      await expect(
+        mergeToBase(result.worktreePath, { baseRef: "main" }, { paseoHome }),
+      ).rejects.toThrow(
+        "No local merge target is recorded for base ref refs/remotes/upstream/main",
+      );
+      expect(
+        execFileSync("git", ["rev-parse", "refs/heads/main"], { cwd: repoDir }).toString().trim(),
+      ).toBe(localMainHead);
+
+      writeFileSync(join(forkCloneDir, "later.txt"), "later\n");
+      execFileSync("git", ["add", "later.txt"], { cwd: forkCloneDir });
+      execFileSync("git", ["-c", "commit.gpgsign=false", "commit", "-m", "advance again"], {
+        cwd: forkCloneDir,
+      });
+      execFileSync("git", ["push", "origin", "main"], { cwd: forkCloneDir });
+      execFileSync("git", ["fetch", "upstream"], { cwd: result.worktreePath });
+      await mergeFromBase(result.worktreePath, { baseRef: "main" }, { paseoHome });
+      expect(readFileSync(join(result.worktreePath, "later.txt"), "utf8")).toBe("later\n");
+
+      execFileSync("git", ["update-ref", "-d", "refs/remotes/upstream/main"], {
+        cwd: result.worktreePath,
+      });
+      await expect(
+        getCheckoutDiff(result.worktreePath, { mode: "base", baseRef: "main" }, { paseoHome }),
+      ).rejects.toThrow("Base ref not found: refs/remotes/upstream/main");
+      await expect(
+        mergeFromBase(result.worktreePath, { baseRef: "main" }, { paseoHome }),
+      ).rejects.toThrow("Base ref not found: refs/remotes/upstream/main");
+      await expect(
+        listCheckoutCommits({ cwd: result.worktreePath, context: { paseoHome } }),
+      ).rejects.toThrow("Base ref not found: refs/remotes/upstream/main");
+    });
+
+    it("records Git-valid characters in a remote base branch", async () => {
+      const upstreamDir = join(tempDir, "upstream.git");
+      execFileSync("git", ["init", "--bare", upstreamDir]);
+      execFileSync("git", ["remote", "add", "upstream", upstreamDir], { cwd: repoDir });
+      execFileSync("git", ["push", "upstream", "refs/heads/main:refs/heads/release+hotfix"], {
+        cwd: repoDir,
+      });
+      execFileSync("git", ["fetch", "upstream"], { cwd: repoDir });
+
+      const result = await createLegacyWorktreeForTest({
+        branchName: "release-hotfix-feature",
+        cwd: repoDir,
+        baseBranch: "refs/remotes/upstream/release+hotfix",
+        worktreeSlug: "release-hotfix-feature",
+        runSetup: false,
+        paseoHome,
+      });
+
+      expect(
+        JSON.parse(readFileSync(getPaseoWorktreeMetadataPath(result.worktreePath), "utf8")),
+      ).toMatchObject({
+        baseRefName: "release+hotfix",
+        baseRef: "refs/remotes/upstream/release+hotfix",
+      });
+    });
+
     it("uses a local branch when origin/{branch} does not exist", async () => {
       writeFileSync(join(repoDir, "file.txt"), "from-local-only\n");
       execFileSync("git", ["add", "file.txt"], { cwd: repoDir });

packages/server/src/utils/worktree.ts

@@ -1271,6 +1271,7 @@ export const createWorktree = async ({
 
   writePaseoWorktreeMetadata(worktreePath, {
     baseRefName: sourcePlan.metadataBaseRefName,
+    ...(sourcePlan.metadataBaseRef ? { baseRef: sourcePlan.metadataBaseRef } : {}),
     ...(sourcePlan.changeRequestLookupTarget
       ? { changeRequestLookupTarget: sourcePlan.changeRequestLookupTarget }
       : {}),
@@ -1300,7 +1301,11 @@ interface ResolveWorktreeSourcePlanOptions {
 
 interface WorktreeSourcePlan {
   branchName: string;
+  // Display name and exact ref are two different facts. The name cannot round-trip to a
+  // commit — "main" resolves local-first even when the worktree was cut from a fork's
+  // upstream — so comparisons and actions read the ref and the UI reads the name.
   metadataBaseRefName: string;
+  metadataBaseRef?: string;
   changeRequestLookupTarget?: PaseoWorktreeChangeRequestHint;
   addArguments: string[];
   pushRemote?: {
@@ -1334,6 +1339,7 @@ async function resolveWorktreeSourcePlan({
       return {
         branchName: newBranchName,
         metadataBaseRefName: normalizedBaseBranch,
+        metadataBaseRef: resolvedBaseBranch,
         addArguments: ["-b", newBranchName, "--no-track", base],
       };
     }