diff --git a/Makefile b/Makefile
index c60d9b9b..743137df 100644
--- a/Makefile
+++ b/Makefile
@@ -31,6 +31,7 @@ help:
 	@echo "  make start-daemon    - Start prod services in background (daemon mode)"
 	@echo "  make stop            - Stop all running services"
 	@echo "  make clean           - Clean up processes and temporary files"
+	@echo "  make migrate-paths   - Migrate legacy users/ tree into workspaces/ layout (DRY_RUN=1 to preview)"
 	@echo ""
 	@echo "Docker Production Commands:"
 	@echo "  make up              - Build and start production Docker services (localhost:2026)"
@@ -144,6 +145,14 @@ clean: stop
 	@-rm -rf logs/*.log 2>/dev/null || true
 	@echo "✓ Cleanup complete"
 
+# Lift legacy per-user paths into the per-workspace layout (PR6).
+# Pass DRY_RUN=1 to log the migration plan without writing.
+# DEFAULT_WORKSPACE=<wid> claims un-assigned users (defaults to legacy_workspace).
+migrate-paths:
+	@cd backend && PYTHONPATH=. uv run python scripts/migrate_paths_to_workspace.py \
+		$(if $(filter 1 true,$(DRY_RUN)),--dry-run) \
+		$(if $(DEFAULT_WORKSPACE),--default-workspace $(DEFAULT_WORKSPACE))
+
 # ==========================================
 # Docker Development Commands
 # ==========================================
diff --git a/backend/app/gateway/app.py b/backend/app/gateway/app.py
index 985bb96c..1f0684fa 100644
--- a/backend/app/gateway/app.py
+++ b/backend/app/gateway/app.py
@@ -175,6 +175,34 @@ async def _migrate_orphaned_threads(store, admin_user_id: str) -> int:
     return migrated
 
 
+def _check_path_migration_pending(app: FastAPI) -> None:
+    """Warn the operator if the PR4 legacy user-isolation layout still has content.
+
+    PR6 routes every new write into ``{base_dir}/workspaces/{wid}/...`` via
+    ``Paths``. Pre-PR6 installations have data at
+    ``{base_dir}/users/{uid}/...`` that needs ``make migrate-paths`` to lift
+    it under a workspace. We emit a warning at boot rather than crashing so
+    the gateway keeps serving (reads from the legacy tree still work via the
+    user_id branch of ``Paths.thread_dir``), but with a loud signal to run
+    the migration script.
+    """
+    from deerflow.config.paths import get_paths
+
+    legacy_users = get_paths().base_dir / "users"
+    if not legacy_users.exists():
+        return
+    try:
+        has_content = any(legacy_users.iterdir())
+    except OSError:
+        # Permission or transient FS issue — don't escalate; lifespan must succeed.
+        return
+    if has_content:
+        logger.warning(
+            "Legacy per-user layout detected at %s. Run `make migrate-paths` to lift it under the per-workspace layout (PR6).",
+            legacy_users,
+        )
+
+
 @asynccontextmanager
 async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
     """Application lifespan handler."""
@@ -191,6 +219,8 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
     config = get_gateway_config()
     logger.info(f"Starting API Gateway on {config.host}:{config.port}")
 
+    _check_path_migration_pending(app)
+
     # Initialize LangGraph runtime components (StreamBridge, RunManager, checkpointer, store)
     async with langgraph_runtime(app):
         logger.info("LangGraph runtime initialised")
diff --git a/backend/tests/test_path_migration_pending_warning.py b/backend/tests/test_path_migration_pending_warning.py
new file mode 100644
index 00000000..c528792d
--- /dev/null
+++ b/backend/tests/test_path_migration_pending_warning.py
@@ -0,0 +1,45 @@
+"""PR6 T6.14 — lifespan warns when legacy users/ tree still has content."""
+
+from __future__ import annotations
+
+import logging
+from pathlib import Path
+from unittest.mock import patch
+
+import pytest
+
+from app.gateway.app import _check_path_migration_pending
+
+
+class _FakePaths:
+    def __init__(self, base: Path):
+        self.base_dir = base
+
+
+@pytest.fixture
+def base(tmp_path: Path) -> Path:
+    return tmp_path
+
+
+def _patch_paths(base: Path):
+    return patch("deerflow.config.paths.get_paths", return_value=_FakePaths(base))
+
+
+def test_warns_when_legacy_users_dir_has_content(base: Path, caplog: pytest.LogCaptureFixture):
+    (base / "users" / "alice" / "threads" / "t1").mkdir(parents=True)
+    with _patch_paths(base), caplog.at_level(logging.WARNING, logger="app.gateway.app"):
+        _check_path_migration_pending(app=None)  # type: ignore[arg-type]
+    assert any("make migrate-paths" in rec.message for rec in caplog.records)
+
+
+def test_silent_when_legacy_users_dir_missing(base: Path, caplog: pytest.LogCaptureFixture):
+    with _patch_paths(base), caplog.at_level(logging.WARNING, logger="app.gateway.app"):
+        _check_path_migration_pending(app=None)  # type: ignore[arg-type]
+    assert not any("migrate-paths" in rec.message for rec in caplog.records)
+
+
+def test_silent_when_legacy_users_dir_empty(base: Path, caplog: pytest.LogCaptureFixture):
+    (base / "users").mkdir()
+    with _patch_paths(base), caplog.at_level(logging.WARNING, logger="app.gateway.app"):
+        _check_path_migration_pending(app=None)  # type: ignore[arg-type]
+    assert not any("migrate-paths" in rec.message for rec in caplog.records)