diff --git a/script/upstream/utils/git.ts b/script/upstream/utils/git.ts
index a781276e983..a04f513e5e5 100644
--- a/script/upstream/utils/git.ts
+++ b/script/upstream/utils/git.ts
@@ -4,6 +4,10 @@
  */
 
 import { $ } from "bun"
+import { rm } from "node:fs/promises"
+import { randomUUID } from "node:crypto"
+import { tmpdir } from "node:os"
+import { join } from "node:path"
 
 export interface BranchInfo {
   current: string
@@ -267,6 +271,11 @@ export async function ensureRerere(): Promise<void> {
   await $`git config rerere.autoupdate true`.quiet()
 }
 
+async function reset(dir: string): Promise<void> {
+  await $`git -C ${dir} reset -q --hard`.quiet().nothrow()
+  await $`git -C ${dir} clean -fdx`.quiet().nothrow()
+}
+
 /**
  * Train the rerere cache from past merge commits in the repo history.
  * Implements the same logic as git's contrib/rerere-train.sh:
@@ -277,14 +286,14 @@ export async function ensureRerere(): Promise<void> {
  * Returns the number of resolutions learned.
  */
 export async function trainRerere(grep: string): Promise<number> {
-  // Save the current HEAD so we can restore it afterwards
-  const headResult = await $`git symbolic-ref -q HEAD`.quiet().nothrow()
-  const branch = headResult.exitCode === 0 ? headResult.stdout.toString().trim() : null
-  const originalHead = branch ?? (await $`git rev-parse --verify HEAD`.text()).trim()
+  const head = (await $`git rev-parse --verify HEAD`.text()).trim()
+  const dir = join(tmpdir(), `kilo-rerere-train-${randomUUID()}`)
 
   let learned = 0
 
   try {
+    await $`git worktree add --detach ${dir} ${head}`.quiet()
+
     // Find all merge commits matching the grep pattern (merges have multiple parents)
     const revList = await $`git rev-list --parents --all --grep=${grep}`.quiet().nothrow()
     if (revList.exitCode !== 0 || !revList.stdout.toString().trim()) return 0
@@ -301,45 +310,45 @@ export async function trainRerere(grep: string): Promise<number> {
 
       const [commit, parent1, ...otherParents] = parts
 
+      await reset(dir)
+
       // Checkout the first parent
-      const coResult = await $`git checkout -q ${parent1}`.quiet().nothrow()
+      const coResult = await $`git -C ${dir} checkout -q ${parent1}`.quiet().nothrow()
       if (coResult.exitCode !== 0) continue
 
       // Attempt the merge - we expect it to fail with conflicts
-      const mergeResult = await $`git merge --no-gpg-sign ${otherParents}`.quiet().nothrow()
+      const mergeResult = await $`git -C ${dir} merge --no-gpg-sign ${otherParents}`.quiet().nothrow()
       if (mergeResult.exitCode === 0) {
         // Cleanly merged — no conflicts to learn from, reset and skip
-        await $`git reset -q --hard`.quiet().nothrow()
+        await reset(dir)
         continue
       }
 
       // Check if rerere recorded a pre-image (MERGE_RR exists and is non-empty)
-      const mergeRR = Bun.file(`${process.env.GIT_DIR || ".git"}/MERGE_RR`)
-      const hasMergeRR = await mergeRR.exists().catch(() => false)
+      const rr = await $`git -C ${dir} rev-parse --git-path MERGE_RR`.text()
+      const hasMergeRR = await Bun.file(rr.trim())
+        .exists()
+        .catch(() => false)
       if (!hasMergeRR) {
-        await $`git reset -q --hard`.quiet().nothrow()
+        await reset(dir)
         continue
       }
 
       // Record the conflict pre-image
-      await $`git rerere`.quiet().nothrow()
+      await $`git -C ${dir} rerere`.quiet().nothrow()
 
       // Apply the actual resolution by checking out the merge commit's tree
-      await $`git checkout -q ${commit} -- .`.quiet().nothrow()
+      await $`git -C ${dir} checkout -q ${commit} -- .`.quiet().nothrow()
 
       // Record the resolution post-image
-      await $`git rerere`.quiet().nothrow()
+      await $`git -C ${dir} rerere`.quiet().nothrow()
 
       learned++
-      await $`git reset -q --hard`.quiet().nothrow()
+      await reset(dir)
     }
   } finally {
-    // Always restore original branch
-    if (branch) {
-      await $`git checkout ${branch.replace("refs/heads/", "")}`.quiet().nothrow()
-    } else {
-      await $`git checkout ${originalHead}`.quiet().nothrow()
-    }
+    await $`git worktree remove --force ${dir}`.quiet().nothrow()
+    await rm(dir, { recursive: true, force: true })
   }
 
   return learned