fix shutree error

src/app.py

@@ -31,25 +31,47 @@ def _init_submodule() -> None:
         token = os.getenv("GH_TOKEN", "")
         if not token:
             raise RuntimeError("GH_TOKEN secret is not set.")
+
         import shutil
+
+        # Aggressively remove any partial/corrupt lsp directory
         if _LSP_PATH.exists():
-            shutil.rmtree(str(_LSP_PATH))
-        result = subprocess.run(
-            [
-                "git", "clone",
-                "--branch", "0412_train",
-                "--depth", "1",
-                f"https://ehejin:{token}@github.com/batu-el/lsp.git",
-                str(_LSP_PATH),
-            ],
-            capture_output=True, text=True,
-        )
-        print(f"[SUBMODULE] clone stdout: {result.stdout}")
-        print(f"[SUBMODULE] clone stderr: {result.stderr}")
-        print(f"[SUBMODULE] clone returncode: {result.returncode}")
-        print(f"[SUBMODULE] prompts exists after clone: {(_LSP_PATH / 'src' / 'prompts').exists()}")
-        if result.returncode != 0:
-            raise RuntimeError(f"Failed to clone lsp: {result.stderr}")
+            shutil.rmtree(str(_LSP_PATH), ignore_errors=True)
+        # Also nuke any leftover .git/modules/lsp entry
+        git_modules = _BASE / ".git" / "modules" / "lsp"
+        if git_modules.exists():
+            shutil.rmtree(str(git_modules), ignore_errors=True)
+
+        clone_url = f"https://ehejin:{token}@github.com/batu-el/lsp.git"
+
+        for attempt in range(1, 4):
+            print(f"[SUBMODULE] clone attempt {attempt}/3 ...")
+            # Remove any partial clone from previous attempt
+            if _LSP_PATH.exists():
+                shutil.rmtree(str(_LSP_PATH), ignore_errors=True)
+            result = subprocess.run(
+                [
+                    "git", "clone",
+                    "--branch", "0412_train",
+                    "--depth", "1",
+                    clone_url,
+                    str(_LSP_PATH),
+                ],
+                capture_output=True, text=True,
+            )
+            print(f"[SUBMODULE] returncode: {result.returncode}")
+            if result.stderr:
+                # Scrub token from log
+                print(f"[SUBMODULE] stderr: {result.stderr.replace(token, '***')}")
+            if result.returncode == 0 and (_LSP_PATH / "src" / "prompts").exists():
+                print("[SUBMODULE] clone succeeded.")
+                break
+            print(f"[SUBMODULE] attempt {attempt} failed, retrying...")
+        else:
+            raise RuntimeError(
+                f"Failed to clone lsp after 3 attempts. "
+                f"Last stderr: {result.stderr.replace(token, '***')}"
+            )
 
     lsp_src = str(_LSP_PATH / "src")
     if lsp_src not in sys.path: