refactor(workflow-file): phase2 replace remaining imports and remove core.file

Complete phase 2 of the file module migration by replacing the remaining repository-wide legacy imports and deleting the temporary core.file compatibility package introduced in phase 1.

What this commit changes
- Replace legacy core.file.* imports with core.workflow.file.* across:
  - controllers
  - core app/agent/datasource/prompt/rag/tools/variables
  - factories, fields, libs, models, services
  - otel parser integration points
  - unit and integration tests that referenced legacy paths
- Migrate residual runtime usages in app/task pipeline paths that still referenced core.file symbols.
- Update tests and model serialization helpers that relied on old module paths.
- Remove the compatibility bridge package entirely:
  - delete core/file/__init__.py
  - delete core/file/constants.py
  - delete core/file/enums.py
  - delete core/file/file_manager.py
  - delete core/file/helpers.py
  - delete core/file/models.py
  - delete core/file/tool_file_parser.py

Verification
- No Python references to core.file remain ( -> empty).
- Targeted regression tests for migrated file primitives and factory/type flows passed:
  - tests/unit_tests/core/test_file.py
  - tests/unit_tests/factories/test_variable_factory.py
  - tests/unit_tests/services/test_variable_truncator.py

Result
- The repository now uses core.workflow.file as the single canonical file namespace.
- The migration is fully split into two commits: phase 1 compatibility + phase 2 full cutover.

api/core/agent/base_agent_runner.py

@@ -17,7 +17,6 @@ from core.app.entities.app_invoke_entities import (
 )
 from core.callback_handler.agent_tool_callback_handler import DifyAgentCallbackHandler
 from core.callback_handler.index_tool_callback_handler import DatasetIndexToolCallbackHandler
-from core.file import file_manager
 from core.memory.token_buffer_memory import TokenBufferMemory
 from core.model_manager import ModelInstance
 from core.model_runtime.entities import (
@@ -40,6 +39,7 @@ from core.tools.entities.tool_entities import (
 )
 from core.tools.tool_manager import ToolManager
 from core.tools.utils.dataset_retriever_tool import DatasetRetrieverTool
+from core.workflow.file import file_manager
 from extensions.ext_database import db
 from factories import file_factory
 from models.enums import CreatorUserRole

api/core/agent/cot_chat_agent_runner.py

@@ -1,7 +1,6 @@
 import json
 
 from core.agent.cot_agent_runner import CotAgentRunner
-from core.file import file_manager
 from core.model_runtime.entities import (
     AssistantPromptMessage,
     PromptMessage,
@@ -11,6 +10,7 @@ from core.model_runtime.entities import (
 )
 from core.model_runtime.entities.message_entities import ImagePromptMessageContent, PromptMessageContentUnionTypes
 from core.model_runtime.utils.encoders import jsonable_encoder
+from core.workflow.file import file_manager
 
 
 class CotChatAgentRunner(CotAgentRunner):

api/core/agent/fc_agent_runner.py

@@ -7,7 +7,6 @@ from typing import Any, Union
 from core.agent.base_agent_runner import BaseAgentRunner
 from core.app.apps.base_app_queue_manager import PublishFrom
 from core.app.entities.queue_entities import QueueAgentThoughtEvent, QueueMessageEndEvent, QueueMessageFileEvent
-from core.file import file_manager
 from core.model_runtime.entities import (
     AssistantPromptMessage,
     LLMResult,
@@ -25,6 +24,7 @@ from core.model_runtime.entities.message_entities import ImagePromptMessageConte
 from core.prompt.agent_history_prompt_transform import AgentHistoryPromptTransform
 from core.tools.entities.tool_entities import ToolInvokeMeta
 from core.tools.tool_engine import ToolEngine
+from core.workflow.file import file_manager
 from core.workflow.nodes.agent.exc import AgentMaxIterationError
 from models.model import Message