fix(rebase): remove duplicate definitions and update stale module paths

Rebase left duplicate function blocks in worker.py (triple human_message
write causing 3x user messages in /history), deps.py, and prompt.py.
Also update checkpointer imports from the old deerflow.agents.checkpointer
path to deerflow.runtime.checkpointer, and clean up orphaned feedback
props in the frontend message components.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

backend/app/gateway/deps.py

@@ -137,36 +137,6 @@ def get_run_context(request: Request) -> RunContext:
     )
 
 
-async def get_current_user(request: Request) -> str | None:
-    """Extract user identity from request.
-
-    Phase 2: always returns None (no authentication).
-    Phase 3: extract user_id from JWT / session / API key header.
-    """
-    return None
-
-
-get_thread_meta_repo = _require("thread_meta_repo", "Thread metadata store")
-
-
-def get_run_context(request: Request) -> RunContext:
-    """Build a :class:`RunContext` from ``app.state`` singletons.
-
-    Returns a *base* context with infrastructure dependencies.  Callers that
-    need per-run fields (e.g. ``follow_up_to_run_id``) should use
-    ``dataclasses.replace(ctx, follow_up_to_run_id=...)`` before passing it
-    to :func:`run_agent`.
-    """
-    from deerflow.config import get_app_config
-
-    return RunContext(
-        checkpointer=get_checkpointer(request),
-        store=get_store(request),
-        event_store=get_run_event_store(request),
-        run_events_config=getattr(get_app_config(), "run_events", None),
-        thread_meta_repo=get_thread_meta_repo(request),
-    )
-
 
 # ---------------------------------------------------------------------------
 # Auth helpers (used by authz.py and auth middleware)

backend/packages/harness/deerflow/agents/lead_agent/prompt.py

@@ -164,30 +164,6 @@ Skip simple one-off tasks.
 """
 
 
-def _skill_mutability_label(category: str) -> str:
-    return "[custom, editable]" if category == "custom" else "[built-in]"
-
-
-def clear_skills_system_prompt_cache() -> None:
-    _get_cached_skills_prompt_section.cache_clear()
-
-
-def _build_skill_evolution_section(skill_evolution_enabled: bool) -> str:
-    if not skill_evolution_enabled:
-        return ""
-    return """
-## Skill Self-Evolution
-After completing a task, consider creating or updating a skill when:
-- The task required 5+ tool calls to resolve
-- You overcame non-obvious errors or pitfalls
-- The user corrected your approach and the corrected version worked
-- You discovered a non-trivial, recurring workflow
-If you used a skill and encountered issues not covered by it, patch it immediately.
-Prefer patch over edit. Before creating a new skill, confirm with the user first.
-Skip simple one-off tasks.
-"""
-
-
 def _build_subagent_section(max_concurrent: int) -> str:
     """Build the subagent system prompt section with dynamic concurrency limit.
 

backend/packages/harness/deerflow/client.py

@@ -374,7 +374,7 @@ class DeerFlowClient:
         """
         checkpointer = self._checkpointer
         if checkpointer is None:
-            from deerflow.agents.checkpointer.provider import get_checkpointer
+            from deerflow.runtime.checkpointer.provider import get_checkpointer
 
             checkpointer = get_checkpointer()
 
@@ -429,7 +429,7 @@ class DeerFlowClient:
         """
         checkpointer = self._checkpointer
         if checkpointer is None:
-            from deerflow.agents.checkpointer.provider import get_checkpointer
+            from deerflow.runtime.checkpointer.provider import get_checkpointer
 
             checkpointer = get_checkpointer()
 

backend/packages/harness/deerflow/runtime/runs/worker.py

@@ -85,64 +85,6 @@ async def run_agent(
     pre_run_snapshot: dict[str, Any] | None = None
     snapshot_capture_failed = False
 
-    # Initialize RunJournal for event capture
-    journal = None
-    if event_store is not None:
-        from deerflow.runtime.journal import RunJournal
-
-        journal = RunJournal(
-            run_id=run_id,
-            thread_id=thread_id,
-            event_store=event_store,
-            track_token_usage=getattr(run_events_config, "track_token_usage", True),
-        )
-
-        # Write human_message event (model_dump format, aligned with checkpoint)
-        human_msg = _extract_human_message(graph_input)
-        if human_msg is not None:
-            msg_metadata = {}
-            if follow_up_to_run_id:
-                msg_metadata["follow_up_to_run_id"] = follow_up_to_run_id
-            await event_store.put(
-                thread_id=thread_id,
-                run_id=run_id,
-                event_type="human_message",
-                category="message",
-                content=human_msg.model_dump(),
-                metadata=msg_metadata or None,
-            )
-            content = human_msg.content
-            journal.set_first_human_message(content if isinstance(content, str) else str(content))
-
-    # Initialize RunJournal for event capture
-    journal = None
-    if event_store is not None:
-        from deerflow.runtime.journal import RunJournal
-
-        journal = RunJournal(
-            run_id=run_id,
-            thread_id=thread_id,
-            event_store=event_store,
-            track_token_usage=getattr(run_events_config, "track_token_usage", True),
-        )
-
-        # Write human_message event (model_dump format, aligned with checkpoint)
-        human_msg = _extract_human_message(graph_input)
-        if human_msg is not None:
-            msg_metadata = {}
-            if follow_up_to_run_id:
-                msg_metadata["follow_up_to_run_id"] = follow_up_to_run_id
-            await event_store.put(
-                thread_id=thread_id,
-                run_id=run_id,
-                event_type="human_message",
-                category="message",
-                content=human_msg.model_dump(),
-                metadata=msg_metadata or None,
-            )
-            content = human_msg.content
-            journal.set_first_human_message(content if isinstance(content, str) else str(content))
-
     journal = None
 
     # Track whether "events" was requested but skipped

backend/tests/test_checkpointer.py

@@ -178,7 +178,7 @@ class TestAsyncCheckpointer:
     @pytest.mark.anyio
     async def test_sqlite_creates_parent_dir_via_to_thread(self):
         """Async SQLite setup should move mkdir off the event loop."""
-        from deerflow.agents.checkpointer.async_provider import make_checkpointer
+        from deerflow.runtime.checkpointer.async_provider import make_checkpointer
 
         mock_config = MagicMock()
         mock_config.checkpointer = CheckpointerConfig(type="sqlite", connection_string="relative/test.db")
@@ -195,11 +195,11 @@ class TestAsyncCheckpointer:
         mock_module.AsyncSqliteSaver = mock_saver_cls
 
         with (
-            patch("deerflow.agents.checkpointer.async_provider.get_app_config", return_value=mock_config),
+            patch("deerflow.runtime.checkpointer.async_provider.get_app_config", return_value=mock_config),
             patch.dict(sys.modules, {"langgraph.checkpoint.sqlite.aio": mock_module}),
-            patch("deerflow.agents.checkpointer.async_provider.asyncio.to_thread", new_callable=AsyncMock) as mock_to_thread,
+            patch("deerflow.runtime.checkpointer.async_provider.asyncio.to_thread", new_callable=AsyncMock) as mock_to_thread,
             patch(
-                "deerflow.agents.checkpointer.async_provider.resolve_sqlite_conn_str",
+                "deerflow.runtime.checkpointer.async_provider.resolve_sqlite_conn_str",
                 return_value="/tmp/resolved/test.db",
             ),
         ):

backend/tests/test_client.py

@@ -1015,7 +1015,7 @@ class TestThreadQueries:
         mock_checkpointer = MagicMock()
         mock_checkpointer.list.return_value = []
 
-        with patch("deerflow.agents.checkpointer.provider.get_checkpointer", return_value=mock_checkpointer):
+        with patch("deerflow.runtime.checkpointer.provider.get_checkpointer", return_value=mock_checkpointer):
             # No internal checkpointer, should fetch from provider
             result = client.list_threads()
 
@@ -1069,7 +1069,7 @@ class TestThreadQueries:
         mock_checkpointer = MagicMock()
         mock_checkpointer.list.return_value = []
 
-        with patch("deerflow.agents.checkpointer.provider.get_checkpointer", return_value=mock_checkpointer):
+        with patch("deerflow.runtime.checkpointer.provider.get_checkpointer", return_value=mock_checkpointer):
             result = client.get_thread("t99")
 
         assert result["thread_id"] == "t99"

frontend/src/components/workspace/messages/message-list-item.tsx

@@ -39,19 +39,11 @@ export function MessageListItem({
   threadId,
   message,
   isLoading,
-  threadId,
 }: {
   className?: string;
-  threadId?: string;
+  threadId: string;
   message: Message;
   isLoading?: boolean;
-  threadId: string;
-  // ``feedback`` is ``undefined`` for messages that are not feedback-eligible
-  // (non-final AI messages, humans, tool results). It is ``null`` for the
-  // final ai_message of a run that has no rating yet, and a FeedbackData
-  // object once rated. The button renders whenever the field is present.
-  feedback?: FeedbackData | null;
-  runId?: string;
 }) {
   const isHuman = message.type === "human";
   return (
@@ -80,13 +72,6 @@ export function MessageListItem({
                 ""
               }
             />
-            {feedback !== undefined && runId && threadId && (
-              <FeedbackButtons
-                threadId={threadId}
-                runId={runId}
-                initialFeedback={feedback}
-              />
-            )}
           </div>
         </MessageToolbar>
       )}

frontend/src/components/workspace/messages/message-list.tsx

@@ -18,7 +18,6 @@ import { useRehypeSplitWordsIntoSpans } from "@/core/rehype";
 import type { Subtask } from "@/core/tasks";
 import { useUpdateSubtask } from "@/core/tasks/context";
 import type { AgentThreadState } from "@/core/threads";
-import { useThreadMessageEnrichment } from "@/core/threads/hooks";
 import { cn } from "@/lib/utils";
 
 import { ArtifactFileList } from "../artifacts/artifact-file-list";
@@ -48,7 +47,6 @@ export function MessageList({
   const rehypePlugins = useRehypeSplitWordsIntoSpans(thread.isLoading);
   const updateSubtask = useUpdateSubtask();
   const messages = thread.messages;
-  const { data: enrichment } = useThreadMessageEnrichment(threadId);
 
   if (thread.isThreadLoading && messages.length === 0) {
     return <MessageListSkeleton />;
@@ -61,21 +59,12 @@ export function MessageList({
         {groupMessages(messages, (group) => {
           if (group.type === "human" || group.type === "assistant") {
             return group.messages.map((msg) => {
-              // Run id and feedback are sourced from the ``/history``
-              // enrichment query (see ``useThreadMessageEnrichment``). The
-              // map is keyed by ``message.id`` so tool_call interleavings
-              // and multi-run threads map cleanly without positional math.
-              // ``feedback`` is ``undefined`` for non-eligible messages,
-              // ``null`` for eligible-but-unrated, and an object once rated.
-              const entry = msg.id ? enrichment?.get(msg.id) : undefined;
               return (
                 <MessageListItem
                   key={`${group.id}/${msg.id}`}
                   threadId={threadId}
                   message={msg}
                   isLoading={thread.isLoading}
-                  runId={entry?.run_id}
-                  feedback={entry?.feedback}
                 />
               );
             });