diff --git a/scripts/ci/auto_fix_formatting.py b/scripts/ci/auto_fix_formatting.py
index 74baed74e..0ec56ad7c 100755
--- a/scripts/ci/auto_fix_formatting.py
+++ b/scripts/ci/auto_fix_formatting.py
@@ -23,6 +23,56 @@ def run(cmd, check=True, capture=True, cwd=None):
     return result
 
 
+def ensure_git_repo(api_url, repo, token, pr_number):
+    """确保当前目录是git仓库，并切换到PR源分支。
+
+    checkout脚本用tarball方式下载代码（PR merge后的commit），没有.git目录。
+    这里自动初始化git仓库，fetch PR源分支并强制checkout，
+    使工作区变为PR源分支的代码，确保后续格式化修复基于源分支。
+    """
+    if os.path.exists(".git"):
+        return
+
+    print("检测到tarball checkout（无.git目录），自动初始化git仓库...")
+
+    # 构造带认证的远端URL
+    server_url = api_url.rsplit("/api/v1", 1)[0]
+    remote_url = f"{server_url.replace('https://', f'https://x-access-token:{token}@')}/{repo}.git"
+
+    # 获取PR的源分支
+    pr_api_url = f"{api_url}/repos/{repo}/pulls/{pr_number}"
+    req_obj = urllib.request.Request(pr_api_url, headers={"Authorization": f"token {token}"})
+    with urllib.request.urlopen(req_obj) as resp:
+        pr = json.loads(resp.read())
+    head_branch = pr["head"]["ref"]
+
+    print(f"PR源分支: {head_branch}")
+
+    # 初始化git
+    run("git init -q")
+    run(f"git remote add origin {remote_url}")
+    run('git config user.name "CI Bot"')
+    run('git config user.email "ci-bot@xiaoxiajianji.com"')
+
+    # fetch源分支（浅克隆，只要最新commit）
+    print("fetch源分支...")
+    run(f"git fetch --depth=1 origin {head_branch}")
+
+    # 强制checkout到源分支（覆盖tarball内容）
+    # tarball是merge后的commit，源分支才是我们要修改并推送的目标
+    print("切换到源分支...")
+    run(f"git checkout -B {head_branch} FETCH_HEAD")
+
+    result = run("git status --porcelain")
+    if result.stdout.strip():
+        n = len(result.stdout.strip().splitlines())
+        print(f"⚠️  工作区有 {n} 个未追踪文件")
+    else:
+        print("✅ git仓库就绪，工作区clean")
+
+    return head_branch
+
+
 def get_changed_files(pr_number, api_url, token):
     """获取PR中变更的文件列表"""
     url = f"{api_url}/pulls/{pr_number}/files?limit=100"
@@ -91,9 +141,7 @@ def fix_frontend(target_fe_files, scan_mode, repo_root):
 
     if scan_mode == "incremental":
         # 增量模式：只格式化变更的前端文件
-        # 转换为相对于 apps/web 的路径或用绝对路径
         target_str = " ".join(target_fe_files)
-        # 从项目根目录运行，prettier 会找配置文件
         cmd = f"{prettier_bin} --write {target_str}"
     else:
         # 全量模式：格式化整个前端目录
@@ -130,6 +178,10 @@ def main():
 
     repo_root = os.getcwd()
 
+    # 确保git仓库可用（tarball checkout模式下自动初始化）
+    # 返回PR源分支名，供后续推送使用
+    head_branch = ensure_git_repo(api_url, repo, token, pr_number)
+
     print("=== 检测到代码格式问题，尝试自动修复 ===")
     print(f"PR #{pr_number}")
     print(f"扫描模式: {scan_mode}")
@@ -149,7 +201,6 @@ def main():
         ".yaml",
         ".yml",
     )
-    # Python 文件扩展名
     py_extensions = (".py",)
 
     # 确定要修复的文件范围
@@ -160,15 +211,13 @@ def main():
         print(f"增量模式: {len(target_py_files)} 个Python文件, {len(target_fe_files)} 个前端文件")
     else:
         target_py_files = ["alembic", "apps", "packages", "tests", "scripts"]
-        # 全量模式下 prettier 在前端目录内部运行，无需传文件列表
-        target_fe_files = ["apps/web"]  # 标记为有前端文件需要处理
+        target_fe_files = ["apps/web"]
         print("全量模式，修复所有文件")
 
     # Python 格式化
     fix_python(target_py_files, scan_mode)
 
     # 前端格式化
-    # 全量模式下直接传 web 目录标记
     if scan_mode != "incremental":
         fix_frontend(["apps/web"], scan_mode, repo_root)
     else:
@@ -186,16 +235,11 @@ def main():
     for line in result.stdout.strip().split("\n"):
         print(f"  {line}")
 
-    # 配置git
-    run('git config user.name "CI Bot"')
-    run('git config user.email "ci-bot@xiaoxiajianji.com"')
-
     # 提交修复
     run("git add -A")
     run('git commit -m "style: auto-format with black + isort + prettier [ci skip]"')
 
-    # 获取来源分支并推送
-    head_branch = get_pr_head_branch(pr_number, f"{api_url}/repos/{repo}", token)
+    # 推送（head_branch已从ensure_git_repo获取）
     print(f"\nPR来源分支: {head_branch}")
 
     run(f'git push origin "HEAD:{head_branch}"')
diff --git a/scripts/ci/run_validate.sh b/scripts/ci/run_validate.sh
index f39279abe..543f1848f 100755
--- a/scripts/ci/run_validate.sh
+++ b/scripts/ci/run_validate.sh
@@ -100,7 +100,11 @@ if [ "$SCAN_MODE" = "incremental" ]; then
   EXISTING_PY_FILES=""
   for f in $CHANGED_PY_FILES; do
     if [ -f "$f" ]; then
-      EXISTING_PY_FILES="$EXISTING_PY_FILES $f"
+      if [ -z "$EXISTING_PY_FILES" ]; then
+        EXISTING_PY_FILES="$f"
+      else
+        EXISTING_PY_FILES="$EXISTING_PY_FILES $f"
+      fi
     fi
   done
   CHANGED_PY_FILES="$EXISTING_PY_FILES"
@@ -108,7 +112,7 @@ if [ "$SCAN_MODE" = "incremental" ]; then
   python3 -m compileall -q $CHANGED_PY_FILES
   python3 -m black --check --fast $CHANGED_PY_FILES
   python3 -m isort --check-only $CHANGED_PY_FILES
-  RUFF_FILES=$(echo "$CHANGED_PY_FILES" | tr ' ' '\n' | grep -v '^scripts/' | tr '\n' ' ')
+  RUFF_FILES=$(echo "$CHANGED_PY_FILES" | tr ' ' '\n' | grep -v '^scripts/' | grep -v '^$' | xargs)
   if [ -n "$RUFF_FILES" ]; then
     python3 -m ruff check $RUFF_FILES --statistics
   else