fix: resolve import errors and test failures after segment 4 merge

- Update BaseNodeData import path to dify_graph.entities.base_node_data
- Change NodeType.COMMAND/FILE_UPLOAD to BuiltinNodeTypes constants
- Fix system_oauth_encryption -> system_encryption rename in commands
- Remove tests for deleted agent runner modules
- Fix Avatar: named import + string size API in collaboration files
- Add missing skill feature deps: @monaco-editor/react, react-arborist,
  @tanstack/react-virtual
- Fix frontend test mocks: add useUserProfile, useLeaderRestoreListener,
  next/navigation mock, and nodeOutputVars to expected payload

Made-with: Cursor

api/dify_graph/graph/graph.py

@@ -286,7 +286,6 @@ class Graph:
             if node_config.get("data", {}).get("type", "") != "group"
         ]
 
-
         # Parse node configurations
         node_configs_map = cls._parse_node_configs(node_configs)
 

api/dify_graph/nodes/agent/agent_node.py

@@ -4,6 +4,7 @@ import json
 from collections.abc import Generator, Mapping, Sequence
 from typing import TYPE_CHECKING, Any, cast
 
+from dify_graph.nodes.agent.entities import AgentNodeData, AgentOldVersionModelFeatures, ParamsAutoGenerated
 from packaging.version import Version
 from pydantic import ValidationError
 from sqlalchemy import select
@@ -48,7 +49,6 @@ from dify_graph.node_events import (
     StreamChunkEvent,
     StreamCompletedEvent,
 )
-from dify_graph.nodes.agent.entities import AgentNodeData, AgentOldVersionModelFeatures, ParamsAutoGenerated
 from dify_graph.nodes.base.node import Node
 from dify_graph.nodes.base.variable_template_parser import VariableTemplateParser
 from dify_graph.runtime import VariablePool

api/dify_graph/nodes/base/entities.py

@@ -57,8 +57,6 @@ class OutputVariableEntity(BaseModel):
         return v
 
 
-
-
 class BaseIterationNodeData(BaseNodeData):
     start_node_id: str | None = None
 

api/dify_graph/nodes/llm/node.py

@@ -31,7 +31,6 @@ from core.memory.base import BaseMemory
 from core.model_manager import ModelInstance
 from core.prompt.entities.advanced_prompt_entities import CompletionModelPromptTemplate, MemoryConfig
 from core.prompt.utils.prompt_message_util import PromptMessageUtil
-from core.rag.entities.citation_metadata import RetrievalSourceMetadata
 from core.sandbox import Sandbox
 from core.sandbox.bash.session import MAX_OUTPUT_FILE_SIZE, MAX_OUTPUT_FILES, SandboxBashSession
 from core.sandbox.entities.config import AppAssets

api/dify_graph/nodes/tool/tool_node.py

@@ -1,4 +1,3 @@
-import logging
 from collections.abc import Generator, Mapping, Sequence
 from typing import TYPE_CHECKING, Any