Refa: Clean the folders. (#12890)

### Type of change

- [x] Refactoring

api/apps/plugin_app.py

@@ -18,7 +18,7 @@
 from quart import Response
 from api.apps import login_required
 from api.utils.api_utils import get_json_result
-from plugin import GlobalPluginManager
+from agent.plugin import GlobalPluginManager
 
 
 @manager.route('/llm_tools', methods=['GET'])  # noqa: F821

api/db/services/dialog_service.py

@@ -35,7 +35,7 @@ from api.db.services.llm_service import LLMBundle
 from common.metadata_utils import apply_meta_data_filter
 from api.db.services.tenant_llm_service import TenantLLMService
 from common.time_utils import current_timestamp, datetime_format
-from graphrag.general.mind_map_extractor import MindMapExtractor
+from rag.graphrag.general.mind_map_extractor import MindMapExtractor
 from rag.advanced_rag import DeepResearcher
 from rag.app.tag import label_question
 from rag.nlp.search import index_name

api/db/services/document_service.py

@@ -1077,7 +1077,7 @@ def doc_upload_and_parse(conversation_id, file_objs, user_id):
         cks = [c for c in docs if c["doc_id"] == doc_id]
 
         if parser_ids[doc_id] != ParserType.PICTURE.value:
-            from graphrag.general.mind_map_extractor import MindMapExtractor
+            from rag.graphrag.general.mind_map_extractor import MindMapExtractor
             mindmap = MindMapExtractor(llm_bdl)
             try:
                 mind_map = asyncio.run(mindmap([c["content_with_weight"] for c in docs if c["doc_id"] == doc_id]))

api/ragflow_server.py

@@ -41,7 +41,7 @@ from common.versions import get_ragflow_version
 from common.config_utils import show_configs
 from common.mcp_tool_call_conn import shutdown_all_mcp_sessions
 from common.log_utils import init_root_logger
-from plugin import GlobalPluginManager
+from agent.plugin import GlobalPluginManager
 from rag.utils.redis_conn import RedisDistributedLock
 
 stop_event = threading.Event()