feat(isolation): wire user_id through all Paths and memory callsites

Pass user_id=get_effective_user_id() at every callsite that invokes
Paths methods or memory functions, enabling per-user filesystem isolation
throughout the harness and app layers.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

backend/app/gateway/routers/memory.py

@@ -13,6 +13,7 @@ from deerflow.agents.memory.updater import (
     update_memory_fact,
 )
 from deerflow.config.memory_config import get_memory_config
+from deerflow.runtime.user_context import get_effective_user_id
 
 router = APIRouter(prefix="/api", tags=["memory"])
 
@@ -147,7 +148,7 @@ async def get_memory() -> MemoryResponse:
         }
         ```
     """
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -167,7 +168,7 @@ async def reload_memory() -> MemoryResponse:
     Returns:
         The reloaded memory data.
     """
-    memory_data = reload_memory_data()
+    memory_data = reload_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -181,7 +182,7 @@ async def reload_memory() -> MemoryResponse:
 async def clear_memory() -> MemoryResponse:
     """Clear all persisted memory data."""
     try:
-        memory_data = clear_memory_data()
+        memory_data = clear_memory_data(user_id=get_effective_user_id())
     except OSError as exc:
         raise HTTPException(status_code=500, detail="Failed to clear memory data.") from exc
 
@@ -202,6 +203,7 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
             content=request.content,
             category=request.category,
             confidence=request.confidence,
+            user_id=get_effective_user_id(),
         )
     except ValueError as exc:
         raise _map_memory_fact_value_error(exc) from exc
@@ -221,7 +223,7 @@ async def create_memory_fact_endpoint(request: FactCreateRequest) -> MemoryRespo
 async def delete_memory_fact_endpoint(fact_id: str) -> MemoryResponse:
     """Delete a single fact from memory by fact id."""
     try:
-        memory_data = delete_memory_fact(fact_id)
+        memory_data = delete_memory_fact(fact_id, user_id=get_effective_user_id())
     except KeyError as exc:
         raise HTTPException(status_code=404, detail=f"Memory fact '{fact_id}' not found.") from exc
     except OSError as exc:
@@ -245,6 +247,7 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
             content=request.content,
             category=request.category,
             confidence=request.confidence,
+            user_id=get_effective_user_id(),
         )
     except ValueError as exc:
         raise _map_memory_fact_value_error(exc) from exc
@@ -265,7 +268,7 @@ async def update_memory_fact_endpoint(fact_id: str, request: FactPatchRequest) -
 )
 async def export_memory() -> MemoryResponse:
     """Export the current memory data."""
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
     return MemoryResponse(**memory_data)
 
 
@@ -279,7 +282,7 @@ async def export_memory() -> MemoryResponse:
 async def import_memory(request: MemoryResponse) -> MemoryResponse:
     """Import and persist memory data."""
     try:
-        memory_data = import_memory_data(request.model_dump())
+        memory_data = import_memory_data(request.model_dump(), user_id=get_effective_user_id())
     except OSError as exc:
         raise HTTPException(status_code=500, detail="Failed to import memory data.") from exc
 
@@ -337,7 +340,7 @@ async def get_memory_status() -> MemoryStatusResponse:
         Combined memory configuration and current data.
     """
     config = get_memory_config()
-    memory_data = get_memory_data()
+    memory_data = get_memory_data(user_id=get_effective_user_id())
 
     return MemoryStatusResponse(
         config=MemoryConfigResponse(