diff --git a/packages/server/src/server/agent/providers/claude-agent.ts b/packages/server/src/server/agent/providers/claude-agent.ts
index f9124ba55..abfb21fdb 100644
--- a/packages/server/src/server/agent/providers/claude-agent.ts
+++ b/packages/server/src/server/agent/providers/claude-agent.ts
@@ -365,7 +365,7 @@ type ClaudeAgentSessionOptions = {
 
 function whichClaude(): string | null {
   try {
-    return execSync("which claude", { encoding: "utf8", env: process.env }).trim() || null;
+    return execSync("which claude", { encoding: "utf8" }).trim() || null;
   } catch {
     return null;
   }
diff --git a/packages/server/src/utils/checkout-git.test.ts b/packages/server/src/utils/checkout-git.test.ts
index cc9f82994..40914e467 100644
--- a/packages/server/src/utils/checkout-git.test.ts
+++ b/packages/server/src/utils/checkout-git.test.ts
@@ -6,6 +6,7 @@ import { tmpdir } from "os";
 import {
   commitAll,
   getCheckoutDiff,
+  getCheckoutShortstat,
   getPullRequestStatus,
   getCheckoutStatus,
   getCheckoutStatusLite,
@@ -138,6 +139,39 @@ describe("checkout git utilities", () => {
     expect(divergedStatus.behindOfOrigin).toBe(1);
   });
 
+  it("uses the freshest comparison base for status and shortstat when local main is stale", async () => {
+    const remoteDir = join(tempDir, "remote.git");
+    const cloneDir = join(tempDir, "clone");
+    execSync(`git init --bare -b main ${remoteDir}`);
+    execSync(`git remote add origin ${remoteDir}`, { cwd: repoDir });
+    execSync("git push -u origin main", { cwd: repoDir });
+
+    execSync(`git clone ${remoteDir} ${cloneDir}`);
+    execSync("git config user.email 'test@test.com'", { cwd: cloneDir });
+    execSync("git config user.name 'Test'", { cwd: cloneDir });
+    writeFileSync(join(cloneDir, "upstream.txt"), "upstream 1\nupstream 2\n");
+    execSync("git add upstream.txt", { cwd: cloneDir });
+    execSync("git -c commit.gpgsign=false commit -m 'remote update'", { cwd: cloneDir });
+    execSync("git push", { cwd: cloneDir });
+
+    execSync("git fetch origin", { cwd: repoDir });
+    execSync("git checkout -b feature origin/main", { cwd: repoDir });
+    writeFileSync(join(repoDir, "feature.txt"), "feature\n");
+    execSync("git add feature.txt", { cwd: repoDir });
+    execSync("git -c commit.gpgsign=false commit -m 'feature update'", { cwd: repoDir });
+
+    const status = await getCheckoutStatus(repoDir);
+    expect(status.isGit).toBe(true);
+    if (!status.isGit) {
+      return;
+    }
+    expect(status.baseRef).toBe("main");
+    expect(status.aheadBehind).toEqual({ ahead: 1, behind: 0 });
+
+    const shortstat = await getCheckoutShortstat(repoDir);
+    expect(shortstat).toEqual({ additions: 1, deletions: 0 });
+  });
+
   it("commits messages with quotes safely", async () => {
     const message = `He said "hello" and it's fine`;
     writeFileSync(join(repoDir, "file.txt"), "quoted\n");
diff --git a/packages/server/src/utils/checkout-git.ts b/packages/server/src/utils/checkout-git.ts
index b2a876cf2..40c2c551a 100644
--- a/packages/server/src/utils/checkout-git.ts
+++ b/packages/server/src/utils/checkout-git.ts
@@ -771,7 +771,7 @@ async function doesGitRefExist(cwd: string, fullRef: string): Promise<boolean> {
   }
 }
 
-async function resolveBestBaseRefForMerge(cwd: string, normalizedBaseRef: string): Promise<string> {
+async function resolveBestComparisonBaseRef(cwd: string, normalizedBaseRef: string): Promise<string> {
   const [hasLocal, hasOrigin] = await Promise.all([
     doesGitRefExist(cwd, `refs/heads/${normalizedBaseRef}`),
     doesGitRefExist(cwd, `refs/remotes/origin/${normalizedBaseRef}`),
@@ -811,8 +811,9 @@ async function getAheadBehind(cwd: string, baseRef: string, currentBranch: strin
   if (!normalizedBaseRef || !currentBranch || normalizedBaseRef === currentBranch) {
     return null;
   }
+  const comparisonBaseRef = await resolveBestComparisonBaseRef(cwd, normalizedBaseRef);
   const { stdout } = await execAsync(
-    `git rev-list --left-right --count ${normalizedBaseRef}...${currentBranch}`,
+    `git rev-list --left-right --count ${comparisonBaseRef}...${currentBranch}`,
     { cwd, env: READ_ONLY_GIT_ENV }
   );
   const [behindRaw, aheadRaw] = stdout.trim().split(/\s+/);
@@ -1103,19 +1104,24 @@ export async function getCheckoutShortstat(
   }
 
   const configured = await getConfiguredBaseRefForCwd(cwd, context);
-  const baseRef = configured.baseRef ?? (await resolveBaseRef(cwd));
-  if (!baseRef) {
+  const localBaseRef = configured.baseRef ?? (await resolveBaseRef(cwd));
+  if (!localBaseRef) {
     return null;
   }
 
   const currentBranch = await getCurrentBranch(cwd);
-  if (currentBranch === baseRef) {
+  if (currentBranch === localBaseRef) {
     return null;
   }
 
+  const comparisonBaseRef = await resolveBestComparisonBaseRef(
+    cwd,
+    normalizeLocalBranchRefName(localBaseRef)
+  );
+
   let mergeBase: string;
   try {
-    const { stdout } = await execAsync(`git merge-base HEAD ${baseRef}`, {
+    const { stdout } = await execAsync(`git merge-base HEAD ${comparisonBaseRef}`, {
       cwd,
       env: READ_ONLY_GIT_ENV,
     });
@@ -1128,7 +1134,7 @@ export async function getCheckoutShortstat(
   }
 
   try {
-    const { stdout } = await execAsync(`git diff --shortstat ${mergeBase}`, {
+    const { stdout } = await execAsync(`git diff --shortstat ${mergeBase} HEAD`, {
       cwd,
       env: READ_ONLY_GIT_ENV,
     });
@@ -1180,7 +1186,7 @@ export async function getCheckoutDiff(
     }
 
     const normalizedBaseRef = normalizeLocalBranchRefName(baseRef);
-    const bestBaseRef = await resolveBestBaseRefForMerge(cwd, normalizedBaseRef);
+    const bestBaseRef = await resolveBestComparisonBaseRef(cwd, normalizedBaseRef);
     refForDiff = (await tryResolveMergeBase(cwd, bestBaseRef)) ?? bestBaseRef;
   }
 
@@ -1521,7 +1527,7 @@ export async function mergeFromBase(
   }
 
   const normalizedBaseRef = normalizeLocalBranchRefName(baseRef);
-  const bestBaseRef = await resolveBestBaseRefForMerge(cwd, normalizedBaseRef);
+  const bestBaseRef = await resolveBestComparisonBaseRef(cwd, normalizedBaseRef);
   if (bestBaseRef === currentBranch) {
     return;
   }