refactor(sandbox): extract connection helpers and move run_command to helper module

- Add helpers.py with connection management utilities:
    - with_connection: context manager for connection lifecycle
    - submit_command: execute command and return CommandFuture
    - execute: run command with auto connection, raise on failure
    - try_execute: run command with auto connection, return result

  - Add CommandExecutionError to exec.py for typed error handling
    with access to exit_code, stderr, and full result

  - Remove run_command method from VirtualEnvironment base class
    (now available as submit_command helper)

  - Update all call sites to use new helper functions:
    - sandbox/session.py
    - sandbox/storage/archive_storage.py
    - sandbox/bash/bash_tool.py
    - workflow/nodes/command/node.py

  - Add comprehensive unit tests for helpers with connection reuse

api/core/sandbox/initializer/__init__.py

@@ -0,0 +1,6 @@
+from core.sandbox.initializer.initializer import DifyCliInitializer, SandboxInitializer
+
+__all__ = [
+    "DifyCliInitializer",
+    "SandboxInitializer",
+]

api/core/sandbox/initializer/initializer.py

@@ -0,0 +1,33 @@
+import logging
+from abc import ABC, abstractmethod
+from io import BytesIO
+from pathlib import Path
+
+from core.sandbox.bash.dify_cli import DifyCliLocator
+from core.sandbox.constants import DIFY_CLI_PATH
+from core.virtual_environment.__base.helpers import execute
+from core.virtual_environment.__base.virtual_environment import VirtualEnvironment
+
+logger = logging.getLogger(__name__)
+
+
+class SandboxInitializer(ABC):
+    @abstractmethod
+    def initialize(self, env: VirtualEnvironment) -> None: ...
+
+
+class DifyCliInitializer(SandboxInitializer):
+    def __init__(self, cli_root: str | Path | None = None) -> None:
+        self._locator = DifyCliLocator(root=cli_root)
+
+    def initialize(self, env: VirtualEnvironment) -> None:
+        binary = self._locator.resolve(env.metadata.os, env.metadata.arch)
+        env.upload_file(DIFY_CLI_PATH, BytesIO(binary.path.read_bytes()))
+
+        execute(
+            env,
+            ["chmod", "+x", DIFY_CLI_PATH],
+            timeout=10,
+            error_message="Failed to mark dify CLI as executable",
+        )
+        logger.info("Dify CLI uploaded to sandbox, path=%s", DIFY_CLI_PATH)