fix: only limit fetch depth when the checkout is already shallow (#1647)

restoreConfigFromBase and setupBranch pass --depth to every git fetch. On a
checkout made with fetch-depth: 0 that does not just cap the download: it
truncates the history already present and marks the repository shallow, which
drops the merge base with the base branch. `git log origin/<base>..HEAD` then
silently includes commits that are already merged, and
`git diff origin/<base>...HEAD` fails with "no merge base" — the two commands
the prompt tells Claude to run to scope its work to the PR.

Gate the flag on `git rev-parse --is-shallow-repository`, so a checkout that is
already shallow (the fetch-depth: 1 default) keeps the same depth behaviour and
the fetch savings it was added for, while a full checkout stays full.

Fixes #1642

test/fetch-depth.test.ts

@@ -0,0 +1,107 @@
+import { afterEach, beforeEach, describe, expect, test } from "bun:test";
+import { execFileSync } from "child_process";
+import { mkdtempSync, rmSync, writeFileSync } from "fs";
+import { join } from "path";
+import { setupBranch } from "../src/github/operations/branch";
+import { fetchDepthArgs } from "../src/github/operations/fetch-depth";
+import { createMockContext } from "./mockContext";
+
+const octokits = {
+  rest: {
+    repos: { get: async () => ({ data: { default_branch: "main" } }) },
+    git: { getRef: async () => ({ data: { object: { sha: "abc1234" } } }) },
+  },
+} as any;
+
+const githubData = {
+  contextData: { title: "Add feature", labels: { nodes: [] } },
+} as any;
+
+describe("setupBranch fetch depth", () => {
+  let originalCwd: string;
+  let tempDir = "";
+  let repoDir: string;
+
+  beforeEach(() => {
+    originalCwd = process.cwd();
+    tempDir = mkdtempSync(join("/tmp", "fetch-depth-"));
+    repoDir = join(tempDir, "repo");
+    const remoteDir = join(tempDir, "origin.git");
+
+    execFileSync("git", ["init", "--bare", remoteDir], { stdio: "pipe" });
+    execFileSync("git", ["init", repoDir], { stdio: "pipe" });
+    git(["checkout", "-b", "main"]);
+    git(["config", "user.email", "test@example.com"]);
+    git(["config", "user.name", "Test User"]);
+
+    for (const message of ["first", "second", "third"]) {
+      writeFileSync(join(repoDir, `${message}.txt`), `${message}\n`);
+      git(["add", "."]);
+      git(["commit", "-m", message]);
+    }
+
+    git(["remote", "add", "origin", remoteDir]);
+    git(["push", "-u", "origin", "main"]);
+
+    process.chdir(repoDir);
+  });
+
+  afterEach(() => {
+    process.chdir(originalCwd);
+    if (tempDir) {
+      rmSync(tempDir, { recursive: true, force: true });
+    }
+  });
+
+  for (const useCommitSigning of [false, true]) {
+    test(`keeps the full history of a complete checkout with use_commit_signing: ${useCommitSigning}`, async () => {
+      const context = createMockContext({
+        isPR: false,
+        entityNumber: 7,
+        inputs: { useCommitSigning, branchPrefix: "claude/" },
+      });
+
+      await setupBranch(octokits, githubData, context);
+
+      expect(git(["rev-parse", "--is-shallow-repository"]).trim()).toBe(
+        "false",
+      );
+      expect(git(["rev-list", "--count", "HEAD"]).trim()).toBe("3");
+    });
+  }
+
+  test("still limits the depth on an already shallow checkout", () => {
+    const shallowDir = join(tempDir, "shallow");
+    execFileSync(
+      "git",
+      [
+        "clone",
+        "--depth=1",
+        `file://${join(tempDir, "origin.git")}`,
+        shallowDir,
+      ],
+      { stdio: "pipe" },
+    );
+
+    process.chdir(shallowDir);
+    expect(
+      execFileSync("git", ["rev-parse", "--is-shallow-repository"], {
+        cwd: shallowDir,
+        encoding: "utf8",
+      }).trim(),
+    ).toBe("true");
+    expect(fetchDepthArgs(20)).toEqual(["--depth=20"]);
+  });
+
+  test("drops the depth limit on a complete checkout", () => {
+    expect(fetchDepthArgs(20)).toEqual([]);
+  });
+
+  function git(args: string[]): string {
+    return execFileSync("git", args, {
+      cwd: repoDir,
+      encoding: "utf8",
+      stdio: ["ignore", "pipe", "pipe"],
+    });
+  }
+});