refactor: use services layer and modularize transfer operations

Decouple CLI commands from internal helper logic and consolidate the
core file transfer operations in the service layer to improve library
portability.

- Make MdrsClient subclass MdrsService to inherit resource resolution.
- Remove all deprecated helper methods from BaseCommand.
- Move core upload and download logic to a new transfer module.
- Refactor all CLI commands to route actions through MdrsClient.
- Eliminate circular imports between client and CLI command modules.

mdrsclient/services.py

@@ -1,9 +1,10 @@
-from typing import Any
 import os
 import re
+from typing import Any
 from unicodedata import normalize
 
 from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
+from mdrsclient.cache import CacheInterface
 from mdrsclient.config import ConfigFile
 from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import (
@@ -21,11 +22,11 @@ class MdrsService:
         self.connection = connection
 
     @classmethod
-    def create_connection(cls, remote: str) -> MDRSConnection:
+    def create_connection(cls, remote: str, cache: CacheInterface | None = None) -> MDRSConnection:
         config = ConfigFile(remote)
         if config.url is None:
             raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
-        return MDRSConnection(config.remote, config.url)
+        return MDRSConnection(config.remote, config.url, cache=cache)
 
     def login(self, username: str, password: str) -> tuple[Token, User]:
         user_api = UsersApi(self.connection)