feat(persistence):Unified persistence layer with event store, feedback, and rebase cleanup (#2134)

* feat(persistence): add unified persistence layer with event store, token tracking, and feedback (#1930)

* feat(persistence): add SQLAlchemy 2.0 async ORM scaffold

Introduce a unified database configuration (DatabaseConfig) that
controls both the LangGraph checkpointer and the DeerFlow application
persistence layer from a single `database:` config section.

New modules:
- deerflow.config.database_config — Pydantic config with memory/sqlite/postgres backends
- deerflow.persistence — async engine lifecycle, DeclarativeBase with to_dict mixin, Alembic skeleton
- deerflow.runtime.runs.store — RunStore ABC + MemoryRunStore implementation

Gateway integration initializes/tears down the persistence engine in
the existing langgraph_runtime() context manager. Legacy checkpointer
config is preserved for backward compatibility.

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

* feat(persistence): add RunEventStore ABC + MemoryRunEventStore

Phase 2-A prerequisite for event storage: adds the unified run event
stream interface (RunEventStore) with an in-memory implementation,
RunEventsConfig, gateway integration, and comprehensive tests (27 cases).

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

* feat(persistence): add ORM models, repositories, DB/JSONL event stores, RunJournal, and API endpoints

Phase 2-B: run persistence + event storage + token tracking.

- ORM models: RunRow (with token fields), ThreadMetaRow, RunEventRow
- RunRepository implements RunStore ABC via SQLAlchemy ORM
- ThreadMetaRepository with owner access control
- DbRunEventStore with trace content truncation and cursor pagination
- JsonlRunEventStore with per-run files and seq recovery from disk
- RunJournal (BaseCallbackHandler) captures LLM/tool/lifecycle events,
  accumulates token usage by caller type, buffers and flushes to store
- RunManager now accepts optional RunStore for persistent backing
- Worker creates RunJournal, writes human_message, injects callbacks
- Gateway deps use factory functions (RunRepository when DB available)
- New endpoints: messages, run messages, run events, token-usage
- ThreadCreateRequest gains assistant_id field
- 92 tests pass (33 new), zero regressions

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

* feat(persistence): add user feedback + follow-up run association

Phase 2-C: feedback and follow-up tracking.

- FeedbackRow ORM model (rating +1/-1, optional message_id, comment)
- FeedbackRepository with CRUD, list_by_run/thread, aggregate stats
- Feedback API endpoints: create, list, stats, delete
- follow_up_to_run_id in RunCreateRequest (explicit or auto-detected
  from latest successful run on the thread)
- Worker writes follow_up_to_run_id into human_message event metadata
- Gateway deps: feedback_repo factory + getter
- 17 new tests (14 FeedbackRepository + 3 follow-up association)
- 109 total tests pass, zero regressions

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

* test+config: comprehensive Phase 2 test coverage + deprecate checkpointer config

- config.example.yaml: deprecate standalone checkpointer section, activate
  unified database:sqlite as default (drives both checkpointer + app data)
- New: test_thread_meta_repo.py (14 tests) — full ThreadMetaRepository coverage
  including check_access owner logic, list_by_owner pagination
- Extended test_run_repository.py (+4 tests) — completion preserves fields,
  list ordering desc, limit, owner_none returns all
- Extended test_run_journal.py (+8 tests) — on_chain_error, track_tokens=false,
  middleware no ai_message, unknown caller tokens, convenience fields,
  tool_error, non-summarization custom event
- Extended test_run_event_store.py (+7 tests) — DB batch seq continuity,
  make_run_event_store factory (memory/db/jsonl/fallback/unknown)
- Extended test_phase2b_integration.py (+4 tests) — create_or_reject persists,
  follow-up metadata, summarization in history, full DB-backed lifecycle
- Fixed DB integration test to use proper fake objects (not MagicMock)
  for JSON-serializable metadata
- 157 total Phase 2 tests pass, zero regressions

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

* config: move default sqlite_dir to .deer-flow/data

Keep SQLite databases alongside other DeerFlow-managed data
(threads, memory) under the .deer-flow/ directory instead of a
top-level ./data folder.

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

* refactor(persistence): remove UTFJSON, use engine-level json_serializer + datetime.now()

- Replace custom UTFJSON type with standard sqlalchemy.JSON in all ORM
  models. Add json_serializer=json.dumps(ensure_ascii=False) to all
  create_async_engine calls so non-ASCII text (Chinese etc.) is stored
  as-is in both SQLite and Postgres.
- Change ORM datetime defaults from datetime.now(UTC) to datetime.now(),
  remove UTC imports.

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

* refactor(gateway): simplify deps.py with getter factory + inline repos

- Replace 6 identical getter functions with _require() factory.
- Inline 3 _make_*_repo() factories into langgraph_runtime(), call
  get_session_factory() once instead of 3 times.
- Add thread_meta upsert in start_run (services.py).

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

* feat(docker): add UV_EXTRAS build arg for optional dependencies

Support installing optional dependency groups (e.g. postgres) at
Docker build time via UV_EXTRAS build arg:
  UV_EXTRAS=postgres docker compose build

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

* refactor(journal): fix flush, token tracking, and consolidate tests

RunJournal fixes:
- _flush_sync: retain events in buffer when no event loop instead of
  dropping them; worker's finally block flushes via async flush().
- on_llm_end: add tool_calls filter and caller=="lead_agent" guard for
  ai_message events; mark message IDs for dedup with record_llm_usage.
- worker.py: persist completion data (tokens, message count) to RunStore
  in finally block.

Model factory:
- Auto-inject stream_usage=True for BaseChatOpenAI subclasses with
  custom api_base, so usage_metadata is populated in streaming responses.

Test consolidation:
- Delete test_phase2b_integration.py (redundant with existing tests).
- Move DB-backed lifecycle test into test_run_journal.py.
- Add tests for stream_usage injection in test_model_factory.py.
- Clean up executor/task_tool dead journal references.

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

* feat(events): widen content type to str|dict in all store backends

Allow event content to be a dict (for structured OpenAI-format messages)
in addition to plain strings. Dict values are JSON-serialized for the DB
backend and deserialized on read; memory and JSONL backends handle dicts
natively. Trace truncation now serializes dicts to JSON before measuring.

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

* fix(events): use metadata flag instead of heuristic for dict content detection

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

* feat(converters): add LangChain-to-OpenAI message format converters

Pure functions langchain_to_openai_message, langchain_to_openai_completion,
langchain_messages_to_openai, and _infer_finish_reason for converting
LangChain BaseMessage objects to OpenAI Chat Completions format, used by
RunJournal for event storage. 15 unit tests added.

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

* fix(converters): handle empty list content as null, clean up test

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

* feat(events): human_message content uses OpenAI user message format

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

* feat(events): ai_message uses OpenAI format, add ai_tool_call message event

- ai_message content now uses {"role": "assistant", "content": "..."} format
- New ai_tool_call message event emitted when lead_agent LLM responds with tool_calls
- ai_tool_call uses langchain_to_openai_message converter for consistent format
- Both events include finish_reason in metadata ("stop" or "tool_calls")

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

* feat(events): add tool_result message event with OpenAI tool message format

Cache tool_call_id from on_tool_start keyed by run_id as fallback for on_tool_end,
then emit a tool_result message event (role=tool, tool_call_id, content) after each
successful tool completion.

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

* feat(events): summary content uses OpenAI system message format

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

* feat(events): replace llm_start/llm_end with llm_request/llm_response in OpenAI format

Add on_chat_model_start to capture structured prompt messages as llm_request events.
Replace llm_end trace events with llm_response using OpenAI Chat Completions format.
Track llm_call_index to pair request/response events.

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

* feat(events): add record_middleware method for middleware trace events

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

* test(events): add full run sequence integration test for OpenAI content format

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

* feat(events): align message events with checkpoint format and add middleware tag injection

- Message events (ai_message, ai_tool_call, tool_result, human_message) now use
  BaseMessage.model_dump() format, matching LangGraph checkpoint values.messages
- on_tool_end extracts tool_call_id/name/status from ToolMessage objects
- on_tool_error now emits tool_result message events with error status
- record_middleware uses middleware:{tag} event_type and middleware category
- Summarization custom events use middleware:summarize category
- TitleMiddleware injects middleware:title tag via get_config() inheritance
- SummarizationMiddleware model bound with middleware:summarize tag
- Worker writes human_message using HumanMessage.model_dump()

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

* feat(threads): switch search endpoint to threads_meta table and sync title

- POST /api/threads/search now queries threads_meta table directly,
  removing the two-phase Store + Checkpointer scan approach
- Add ThreadMetaRepository.search() with metadata/status filters
- Add ThreadMetaRepository.update_display_name() for title sync
- Worker syncs checkpoint title to threads_meta.display_name on run completion
- Map display_name to values.title in search response for API compatibility

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

* feat(threads): history endpoint reads messages from event store

- POST /api/threads/{thread_id}/history now combines two data sources:
  checkpointer for checkpoint_id, metadata, title, thread_data;
  event store for messages (complete history, not truncated by summarization)
- Strip internal LangGraph metadata keys from response
- Remove full channel_values serialization in favor of selective fields

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

* fix: remove duplicate optional-dependencies header in pyproject.toml

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

* fix(middleware): pass tagged config to TitleMiddleware ainvoke call

Without the config, the middleware:title tag was not injected,
causing the LLM response to be recorded as a lead_agent ai_message
in run_events.

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

* fix: resolve merge conflict in .env.example

Keep both DATABASE_URL (from persistence-scaffold) and WECOM
credentials (from main) after the merge.

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

* fix(persistence): address review feedback on PR #1851

- Fix naive datetime.now() → datetime.now(UTC) in all ORM models
- Fix seq race condition in DbRunEventStore.put() with FOR UPDATE
  and UNIQUE(thread_id, seq) constraint
- Encapsulate _store access in RunManager.update_run_completion()
- Deduplicate _store.put() logic in RunManager via _persist_to_store()
- Add update_run_completion to RunStore ABC + MemoryRunStore
- Wire follow_up_to_run_id through the full create path
- Add error recovery to RunJournal._flush_sync() lost-event scenario
- Add migration note for search_threads breaking change
- Fix test_checkpointer_none_fix mock to set database=None

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

* chore: update uv.lock

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

* fix(persistence): address 22 review comments from CodeQL, Copilot, and Code Quality

Bug fixes:
- Sanitize log params to prevent log injection (CodeQL)
- Reset threads_meta.status to idle/error when run completes
- Attach messages only to latest checkpoint in /history response
- Write threads_meta on POST /threads so new threads appear in search

Lint fixes:
- Remove unused imports (journal.py, migrations/env.py, test_converters.py)
- Convert lambda to named function (engine.py, Ruff E731)
- Remove unused logger definitions in repos (Ruff F841)
- Add logging to JSONL decode errors and empty except blocks
- Separate assert side-effects in tests (CodeQL)
- Remove unused local variables in tests (Ruff F841)
- Fix max_trace_content truncation to use byte length, not char length

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

* style: apply ruff format to persistence and runtime files

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

* Potential fix for pull request finding 'Statement has no effect'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* refactor(runtime): introduce RunContext to reduce run_agent parameter bloat

Extract checkpointer, store, event_store, run_events_config, thread_meta_repo,
and follow_up_to_run_id into a frozen RunContext dataclass. Add get_run_context()
in deps.py to build the base context from app.state singletons. start_run() uses
dataclasses.replace() to enrich per-run fields before passing ctx to run_agent.

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

* refactor(gateway): move sanitize_log_param to app/gateway/utils.py

Extract the log-injection sanitizer from routers/threads.py into a shared
utils module and rename to sanitize_log_param (public API). Eliminates the
reverse service → router import in services.py.

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

* perf: use SQL aggregation for feedback stats and thread token usage

Replace Python-side counting in FeedbackRepository.aggregate_by_run with
a single SELECT COUNT/SUM query. Add RunStore.aggregate_tokens_by_thread
abstract method with SQL GROUP BY implementation in RunRepository and
Python fallback in MemoryRunStore. Simplify the thread_token_usage
endpoint to delegate to the new method, eliminating the limit=10000
truncation risk.

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

* docs: annotate DbRunEventStore.put() as low-frequency path

Add docstring clarifying that put() opens a per-call transaction with
FOR UPDATE and should only be used for infrequent writes (currently
just the initial human_message event). High-throughput callers should
use put_batch() instead.

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

* fix(threads): fall back to Store search when ThreadMetaRepository is unavailable

When database.backend=memory (default) or no SQL session factory is
configured, search_threads now queries the LangGraph Store instead of
returning 503. Returns empty list if neither Store nor repo is available.

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

* refactor(persistence): introduce ThreadMetaStore ABC for backend-agnostic thread metadata

Add ThreadMetaStore abstract base class with create/get/search/update/delete
interface. ThreadMetaRepository (SQL) now inherits from it. New
MemoryThreadMetaStore wraps LangGraph BaseStore for memory-mode deployments.

deps.py now always provides a non-None thread_meta_repo, eliminating all
`if thread_meta_repo is not None` guards in services.py, worker.py, and
routers/threads.py. search_threads no longer needs a Store fallback branch.

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

* refactor(history): read messages from checkpointer instead of RunEventStore

The /history endpoint now reads messages directly from the
checkpointer's channel_values (the authoritative source) instead of
querying RunEventStore.list_messages(). The RunEventStore API is
preserved for other consumers.

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

* fix(persistence): address new Copilot review comments

- feedback.py: validate thread_id/run_id before deleting feedback
- jsonl.py: add path traversal protection with ID validation
- run_repo.py: parse `before` to datetime for PostgreSQL compat
- thread_meta_repo.py: fix pagination when metadata filter is active
- database_config.py: use resolve_path for sqlite_dir consistency

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

* Implement skill self-evolution and skill_manage flow (#1874)

* chore: ignore .worktrees directory

* Add skill_manage self-evolution flow

* Fix CI regressions for skill_manage

* Address PR review feedback for skill evolution

* fix(skill-evolution): preserve history on delete

* fix(skill-evolution): tighten scanner fallbacks

* docs: add skill_manage e2e evidence screenshot

* fix(skill-manage): avoid blocking fs ops in session runtime

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

* fix(config): resolve sqlite_dir relative to CWD, not Paths.base_dir

resolve_path() resolves relative to Paths.base_dir (.deer-flow),
which double-nested the path to .deer-flow/.deer-flow/data/app.db.
Use Path.resolve() (CWD-relative) instead.

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

* Feature/feishu receive file (#1608)

* feat(feishu): add channel file materialization hook for inbound messages

- Introduce Channel.receive_file(msg, thread_id) as a base method for file materialization; default is no-op.
- Implement FeishuChannel.receive_file to download files/images from Feishu messages, save to sandbox, and inject virtual paths into msg.text.
- Update ChannelManager to call receive_file for any channel if msg.files is present, enabling downstream model access to user-uploaded files.
- No impact on Slack/Telegram or other channels (they inherit the default no-op).

* style(backend): format code with ruff for lint compliance

- Auto-formatted packages/harness/deerflow/agents/factory.py and tests/test_create_deerflow_agent.py using `ruff format`
- Ensured both files conform to project linting standards
- Fixes CI lint check failures caused by code style issues

* fix(feishu): handle file write operation asynchronously to prevent blocking

* fix(feishu): rename GetMessageResourceRequest to _GetMessageResourceRequest and remove redundant code

* test(feishu): add tests for receive_file method and placeholder replacement

* fix(manager): remove unnecessary type casting for channel retrieval

* fix(feishu): update logging messages to reflect resource handling instead of image

* fix(feishu): sanitize filename by replacing invalid characters in file uploads

* fix(feishu): improve filename sanitization and reorder image key handling in message processing

* fix(feishu): add thread lock to prevent filename conflicts during file downloads

* fix(test): correct bad merge in test_feishu_parser.py

* chore: run ruff and apply formatting cleanup
fix(feishu): preserve rich-text attachment order and improve fallback filename handling

* fix(docker): restore gateway env vars and fix langgraph empty arg issue (#1915)

Two production docker-compose.yaml bugs prevent `make up` from working:

1. Gateway missing DEER_FLOW_CONFIG_PATH and DEER_FLOW_EXTENSIONS_CONFIG_PATH
   environment overrides. Added in fb2d99f (#1836) but accidentally reverted
   by ca2fb95 (#1847). Without them, gateway reads host paths from .env via
   env_file, causing FileNotFoundError inside the container.

2. Langgraph command fails when LANGGRAPH_ALLOW_BLOCKING is unset (default).
   Empty $${allow_blocking} inserts a bare space between flags, causing
   ' --no-reload' to be parsed as unexpected extra argument. Fix by building
   args string first and conditionally appending --allow-blocking.

Co-authored-by: cooper <cooperfu@tencent.com>

* fix(frontend): resolve invalid HTML nesting and tabnabbing vulnerabilities (#1904)

* fix(frontend): resolve invalid HTML nesting and tabnabbing vulnerabilities

Fix `<button>` inside `<a>` invalid HTML in artifact components and add
missing `noopener,noreferrer` to `window.open` calls to prevent reverse
tabnabbing.

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

* fix(frontend): address Copilot review on tabnabbing and double-tab-open

Remove redundant parent onClick on web_fetch ChainOfThoughtStep to
prevent opening two tabs on link click, and explicitly null out
window.opener after window.open() for defensive tabnabbing hardening.

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

* refactor(persistence): organize entities into per-entity directories

Restructure the persistence layer from horizontal "models/ + repositories/"
split into vertical entity-aligned directories. Each entity (thread_meta,
run, feedback) now owns its ORM model, abstract interface (where applicable),
and concrete implementations under a single directory with an aggregating
__init__.py for one-line imports.

Layout:
  persistence/thread_meta/{base,model,sql,memory}.py
  persistence/run/{model,sql}.py
  persistence/feedback/{model,sql}.py

models/__init__.py is kept as a facade so Alembic autogenerate continues to
discover all ORM tables via Base.metadata. RunEventRow remains under
models/run_event.py because its storage implementation lives in
runtime/events/store/db.py and has no matching repository directory.

The repositories/ directory is removed entirely. All call sites in
gateway/deps.py and tests are updated to import from the new entity
packages, e.g.:

    from deerflow.persistence.thread_meta import ThreadMetaRepository
    from deerflow.persistence.run import RunRepository
    from deerflow.persistence.feedback import FeedbackRepository

Full test suite passes (1690 passed, 14 skipped).

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

* fix(gateway): sync thread rename and delete through ThreadMetaStore

The POST /threads/{id}/state endpoint previously synced title changes
only to the LangGraph Store via _store_upsert. In sqlite mode the search
endpoint reads from the ThreadMetaRepository SQL table, so renames never
appeared in /threads/search until the next agent run completed (worker.py
syncs title from checkpoint to thread_meta in its finally block).

Likewise the DELETE /threads/{id} endpoint cleaned up the filesystem,
Store, and checkpointer but left the threads_meta row orphaned in sqlite,
so deleted threads kept appearing in /threads/search.

Fix both endpoints by routing through the ThreadMetaStore abstraction
which already has the correct sqlite/memory implementations wired up by
deps.py. The rename path now calls update_display_name() and the delete
path calls delete() — both work uniformly across backends.

Verified end-to-end with curl in gateway mode against sqlite backend.
Existing test suite (1690 passed) and focused router/repo tests pass.

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

* refactor(gateway): route all thread metadata access through ThreadMetaStore

Following the rename/delete bug fix in PR1, migrate the remaining direct
LangGraph Store reads/writes in the threads router and services to the
ThreadMetaStore abstraction so that the sqlite and memory backends behave
identically and the legacy dual-write paths can be removed.

Migrated endpoints (threads.py):
- create_thread: idempotency check + write now use thread_meta_repo.get/create
  instead of dual-writing the LangGraph Store and the SQL row.
- get_thread: reads from thread_meta_repo.get; the checkpoint-only fallback
  for legacy threads is preserved.
- patch_thread: replaced _store_get/_store_put with thread_meta_repo.update_metadata.
- delete_thread_data: dropped the legacy store.adelete; thread_meta_repo.delete
  already covers it.

Removed dead code (services.py):
- _upsert_thread_in_store — redundant with the immediately following
  thread_meta_repo.create() call.
- _sync_thread_title_after_run — worker.py's finally block already syncs
  the title via thread_meta_repo.update_display_name() after each run.

Removed dead code (threads.py):
- _store_get / _store_put / _store_upsert helpers (no remaining callers).
- THREADS_NS constant.
- get_store import (router no longer touches the LangGraph Store directly).

New abstract method:
- ThreadMetaStore.update_metadata(thread_id, metadata) merges metadata into
  the thread's metadata field. Implemented in both ThreadMetaRepository (SQL,
  read-modify-write inside one session) and MemoryThreadMetaStore. Three new
  unit tests cover merge / empty / nonexistent behaviour.

Net change: -134 lines. Full test suite: 1693 passed, 14 skipped.
Verified end-to-end with curl in gateway mode against sqlite backend
(create / patch / get / rename / search / delete).

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

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
Co-authored-by: DanielWalnut <45447813+hetaoBackend@users.noreply.github.com>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Co-authored-by: JilongSun <965640067@qq.com>
Co-authored-by: jie <49781832+stan-fu@users.noreply.github.com>
Co-authored-by: cooper <cooperfu@tencent.com>
Co-authored-by: yangzheli <43645580+yangzheli@users.noreply.github.com>

* feat(auth): release-validation pass for 2.0-rc — 12 blockers + simplify follow-ups (#2008)

* feat(auth): introduce backend auth module

Port RFC-001 authentication core from PR #1728:
- JWT token handling (create_access_token, decode_token, TokenPayload)
- Password hashing (bcrypt) with verify_password
- SQLite UserRepository with base interface
- Provider Factory pattern (LocalAuthProvider)
- CLI reset_admin tool
- Auth-specific errors (AuthErrorCode, TokenError, AuthErrorResponse)

Deps:
- bcrypt>=4.0.0
- pyjwt>=2.9.0
- email-validator>=2.0.0
- backend/uv.toml pins public PyPI index

Tests: 12 pure unit tests (test_auth_config.py, test_auth_errors.py).

Scope note: authz.py, test_auth.py, and test_auth_type_system.py are
deferred to commit 2 because they depend on middleware and deps wiring
that is not yet in place. Commit 1 stays "pure new files only" as the
spec mandates.

* feat(auth): wire auth end-to-end (middleware + frontend replacement)

Backend:
- Port auth_middleware, csrf_middleware, langgraph_auth, routers/auth
- Port authz decorator (owner_filter_key defaults to 'owner_id')
- Merge app.py: register AuthMiddleware + CSRFMiddleware + CORS, add
  _ensure_admin_user lifespan hook, _migrate_orphaned_threads helper,
  register auth router
- Merge deps.py: add get_local_provider, get_current_user_from_request,
  get_optional_user_from_request; keep get_current_user as thin str|None
  adapter for feedback router
- langgraph.json: add auth path pointing to langgraph_auth.py:auth
- Rename metadata['user_id'] -> metadata['owner_id'] in langgraph_auth
  (both metadata write and LangGraph filter dict) + test fixtures

Frontend:
- Delete better-auth library and api catch-all route
- Remove better-auth npm dependency and env vars (BETTER_AUTH_SECRET,
  BETTER_AUTH_GITHUB_*) from env.js
- Port frontend/src/core/auth/* (AuthProvider, gateway-config,
  proxy-policy, server-side getServerSideUser, types)
- Port frontend/src/core/api/fetcher.ts
- Port (auth)/layout, (auth)/login, (auth)/setup pages
- Rewrite workspace/layout.tsx as server component that calls
  getServerSideUser and wraps in AuthProvider
- Port workspace/workspace-content.tsx for the client-side sidebar logic

Tests:
- Port 5 auth test files (test_auth, test_auth_middleware,
  test_auth_type_system, test_ensure_admin, test_langgraph_auth)
- 176 auth tests PASS

After this commit: login/logout/registration flow works, but persistence
layer does not yet filter by owner_id. Commit 4 closes that gap.

* feat(auth): account settings page + i18n

- Port account-settings-page.tsx (change password, change email, logout)
- Wire into settings-dialog.tsx as new "account" section with UserIcon,
  rendered first in the section list
- Add i18n keys:
  - en-US/zh-CN: settings.sections.account ("Account" / "账号")
  - en-US/zh-CN: button.logout ("Log out" / "退出登录")
  - types.ts: matching type declarations

* feat(auth): enforce owner_id across 2.0-rc persistence layer

Add request-scoped contextvar-based owner filtering to threads_meta,
runs, run_events, and feedback repositories. Router code is unchanged
— isolation is enforced at the storage layer so that any caller that
forgets to pass owner_id still gets filtered results, and new routes
cannot accidentally leak data.

Core infrastructure
-------------------
- deerflow/runtime/user_context.py (new):
  - ContextVar[CurrentUser | None] with default None
  - runtime_checkable CurrentUser Protocol (structural subtype with .id)
  - set/reset/get/require helpers
  - AUTO sentinel + resolve_owner_id(value, method_name) for sentinel
    three-state resolution: AUTO reads contextvar, explicit str
    overrides, explicit None bypasses the filter (for migration/CLI)

Repository changes
------------------
- ThreadMetaRepository: create/get/search/update_*/delete gain
  owner_id=AUTO kwarg; read paths filter by owner, writes stamp it,
  mutations check ownership before applying
- RunRepository: put/get/list_by_thread/delete gain owner_id=AUTO kwarg
- FeedbackRepository: create/get/list_by_run/list_by_thread/delete
  gain owner_id=AUTO kwarg
- DbRunEventStore: list_messages/list_events/list_messages_by_run/
  count_messages/delete_by_thread/delete_by_run gain owner_id=AUTO
  kwarg. Write paths (put/put_batch) read contextvar softly: when a
  request-scoped user is available, owner_id is stamped; background
  worker writes without a user context pass None which is valid
  (orphan row to be bound by migration)

Schema
------
- persistence/models/run_event.py: RunEventRow.owner_id = Mapped[
  str | None] = mapped_column(String(64), nullable=True, index=True)
- No alembic migration needed: 2.0 ships fresh, Base.metadata.create_all
  picks up the new column automatically

Middleware
----------
- auth_middleware.py: after cookie check, call get_optional_user_from_
  request to load the real User, stamp it into request.state.user AND
  the contextvar via set_current_user, reset in a try/finally. Public
  paths and unauthenticated requests continue without contextvar, and
  @require_auth handles the strict 401 path

Test infrastructure
-------------------
- tests/conftest.py: @pytest.fixture(autouse=True) _auto_user_context
  sets a default SimpleNamespace(id="test-user-autouse") on every test
  unless marked @pytest.mark.no_auto_user. Keeps existing 20+
  persistence tests passing without modification
- pyproject.toml [tool.pytest.ini_options]: register no_auto_user
  marker so pytest does not emit warnings for opt-out tests
- tests/test_user_context.py: 6 tests covering three-state semantics,
  Protocol duck typing, and require/optional APIs
- tests/test_thread_meta_repo.py: one test updated to pass owner_id=
  None explicitly where it was previously relying on the old default

Test results
------------
- test_user_context.py: 6 passed
- test_auth*.py + test_langgraph_auth.py + test_ensure_admin.py: 127
- test_run_event_store / test_run_repository / test_thread_meta_repo
  / test_feedback: 92 passed
- Full backend suite: 1905 passed, 2 failed (both @requires_llm flaky
  integration tests unrelated to auth), 1 skipped

* feat(auth): extend orphan migration to 2.0-rc persistence tables

_ensure_admin_user now runs a three-step pipeline on every boot:

  Step 1 (fatal):     admin user exists / is created / password is reset
  Step 2 (non-fatal): LangGraph store orphan threads → admin
  Step 3 (non-fatal): SQL persistence tables → admin
    - threads_meta
    - runs
    - run_events
    - feedback

Each step is idempotent. The fatal/non-fatal split mirrors PR #1728's
original philosophy: admin creation failure blocks startup (the system
is unusable without an admin), whereas migration failures log a warning
and let the service proceed (a partial migration is recoverable; a
missing admin is not).

Key helpers
-----------
- _iter_store_items(store, namespace, *, page_size=500):
  async generator that cursor-paginates across LangGraph store pages.
  Fixes PR #1728's hardcoded limit=1000 bug that would silently lose
  orphans beyond the first page.

- _migrate_orphaned_threads(store, admin_user_id):
  Rewritten to use _iter_store_items. Returns the migrated count so the
  caller can log it; raises only on unhandled exceptions.

- _migrate_orphan_sql_tables(admin_user_id):
  Imports the 4 ORM models lazily, grabs the shared session factory,
  runs one UPDATE per table in a single transaction, commits once.
  No-op when no persistence backend is configured (in-memory dev).

Tests: test_ensure_admin.py (8 passed)

* test(auth): port AUTH test plan docs + lint/format pass

- Port backend/docs/AUTH_TEST_PLAN.md and AUTH_UPGRADE.md from PR #1728
- Rename metadata.user_id → metadata.owner_id in AUTH_TEST_PLAN.md
  (4 occurrences from the original PR doc)
- ruff auto-fix UP037 in sentinel type annotations: drop quotes around
  "str | None | _AutoSentinel" now that from __future__ import
  annotations makes them implicit string forms
- ruff format: 2 files (app/gateway/app.py, runtime/user_context.py)

Note on test coverage additions:
- conftest.py autouse fixture was already added in commit 4 (had to
  be co-located with the repository changes to keep pre-existing
  persistence tests passing)
- cross-user isolation E2E tests (test_owner_isolation.py) deferred
  — enforcement is already proven by the 98-test repository suite
  via the autouse fixture + explicit _AUTO sentinel exercises
- New test cases (TC-API-17..20, TC-ATK-13, TC-MIG-01..07) listed
  in AUTH_TEST_PLAN.md are deferred to a follow-up PR — they are
  manual-QA test cases rather than pytest code, and the spec-level
  coverage is already met by test_user_context.py + the 98-test
  repository suite.

Final test results:
- Auth suite (test_auth*, test_langgraph_auth, test_ensure_admin,
  test_user_context): 186 passed
- Persistence suite (test_run_event_store, test_run_repository,
  test_thread_meta_repo, test_feedback): 98 passed
- Lint: ruff check + ruff format both clean

* test(auth): add cross-user isolation test suite

10 tests exercising the storage-layer owner filter by manually
switching the user_context contextvar between two users. Verifies
the safety invariant:

  After a repository write with owner_id=A, a subsequent read with
  owner_id=B must not return the row, and vice versa.

Covers all 4 tables that own user-scoped data:

TC-API-17  threads_meta  — read, search, update, delete cross-user
TC-API-18  runs          — get, list_by_thread, delete cross-user
TC-API-19  run_events    — list_messages, list_events, count_messages,
                           delete_by_thread (CRITICAL: raw conversation
                           content leak vector)
TC-API-20  feedback      — get, list_by_run, delete cross-user

Plus two meta-tests verifying the sentinel pattern itself:
- AUTO + unset contextvar raises RuntimeError
- explicit owner_id=None bypasses the filter (migration escape hatch)

Architecture note
-----------------
These tests bypass the HTTP layer by design. The full chain
(cookie → middleware → contextvar → repository) is covered piecewise:

- test_auth_middleware.py: middleware sets contextvar from cookies
- test_owner_isolation.py: repositories enforce isolation when
  contextvar is set to different users

Together they prove the end-to-end safety property without the
ceremony of spinning up a full TestClient + in-memory DB for every
router endpoint.

Tests pass: 231 (full auth + persistence + isolation suite)
Lint: clean

* refactor(auth): migrate user repository to SQLAlchemy ORM

Move the users table into the shared persistence engine so auth
matches the pattern of threads_meta, runs, run_events, and feedback —
one engine, one session factory, one schema init codepath.

New files
---------
- persistence/user/__init__.py, persistence/user/model.py: UserRow
  ORM class with partial unique index on (oauth_provider, oauth_id)
- Registered in persistence/models/__init__.py so
  Base.metadata.create_all() picks it up

Modified
--------
- auth/repositories/sqlite.py: rewritten as async SQLAlchemy,
  identical constructor pattern to the other four repositories
  (def __init__(self, session_factory) + self._sf = session_factory)
- auth/config.py: drop users_db_path field — storage is configured
  through config.database like every other table
- deps.py/get_local_provider: construct SQLiteUserRepository with
  the shared session factory, fail fast if engine is not initialised
- tests/test_auth.py: rewrite test_sqlite_round_trip_new_fields to
  use the shared engine (init_engine + close_engine in a tempdir)
- tests/test_auth_type_system.py: add per-test autouse fixture that
  spins up a scratch engine and resets deps._cached_* singletons

* refactor(auth): remove SQL orphan migration (unused in supported scenarios)

The _migrate_orphan_sql_tables helper existed to bind NULL owner_id
rows in threads_meta, runs, run_events, and feedback to the admin on
first boot. But in every supported upgrade path, it's a no-op:

  1. Fresh install: create_all builds fresh tables, no legacy rows
  2. No-auth → with-auth (no existing persistence DB): persistence
     tables are created fresh by create_all, no legacy rows
  3. No-auth → with-auth (has existing persistence DB from #1930):
     NOT a supported upgrade path — "有 DB 到有 DB" schema evolution
     is out of scope; users wipe DB or run manual ALTER

So the SQL orphan migration never has anything to do in the
supported matrix. Delete the function, simplify _ensure_admin_user
from a 3-step pipeline to a 2-step one (admin creation + LangGraph
store orphan migration only).

LangGraph store orphan migration stays: it serves the real
"no-auth → with-auth" upgrade path where a user's existing LangGraph
thread metadata has no owner_id field and needs to be stamped with
the newly-created admin's id.

Tests: 284 passed (auth + persistence + isolation)
Lint: clean

* security(auth): write initial admin password to 0600 file instead of logs

CodeQL py/clear-text-logging-sensitive-data flagged 3 call sites that
logged the auto-generated admin password to stdout via logger.info().
Production log aggregators (ELK/Splunk/etc) would have captured those
cleartext secrets. Replace with a shared helper that writes to
.deer-flow/admin_initial_credentials.txt with mode 0600, and log only
the path.

New file
--------
- app/gateway/auth/credential_file.py: write_initial_credentials()
  helper. Takes email, password, and a "initial"/"reset" label.
  Creates .deer-flow/ if missing, writes a header comment plus the
  email+password, chmods 0o600, returns the absolute Path.

Modified
--------
- app/gateway/app.py: both _ensure_admin_user paths (fresh creation
  + needs_setup password reset) now write to file and log the path
- app/gateway/auth/reset_admin.py: rewritten to use the shared ORM
  repo (SQLiteUserRepository with session_factory) and the
  credential_file helper. The previous implementation was broken
  after the earlier ORM refactor — it still imported _get_users_conn
  and constructed SQLiteUserRepository() without a session factory.

No tests changed — the three password-log sites are all exercised
via existing test_ensure_admin.py which checks that startup
succeeds, not that a specific string appears in logs.

CodeQL alerts 272, 283, 284: all resolved.

* security(auth): strict JWT validation in middleware (fix junk cookie bypass)

AUTH_TEST_PLAN test 7.5.8 expects junk cookies to be rejected with
401. The previous middleware behaviour was "presence-only": check
that some access_token cookie exists, then pass through. In
combination with my Task-12 decision to skip @require_auth
decorators on routes, this created a gap where a request with any
cookie-shaped string (e.g. access_token=not-a-jwt) would bypass
authentication on routes that do not touch the repository
(/api/models, /api/mcp/config, /api/memory, /api/skills, …).

Fix: middleware now calls get_current_user_from_request() strictly
and catches the resulting HTTPException to render a 401 with the
proper fine-grained error code (token_invalid, token_expired,
user_not_found, …). On success it stamps request.state.user and
the contextvar so repository-layer owner filters work downstream.

The 4 old "_with_cookie_passes" tests in test_auth_middleware.py
were written for the presence-only behaviour; they asserted that
a junk cookie would make the handler return 200. They are renamed
to "_with_junk_cookie_rejected" and their assertions flipped to
401. The negative path (no cookie → 401 not_authenticated)
is unchanged.

Verified:
  no cookie       → 401 not_authenticated
  junk cookie     → 401 token_invalid     (the fixed bug)
  expired cookie  → 401 token_expired

Tests: 284 passed (auth + persistence + isolation)
Lint: clean

* security(auth): wire @require_permission(owner_check=True) on isolation routes

Apply the require_permission decorator to all 28 routes that take a
{thread_id} path parameter. Combined with the strict middleware
(previous commit), this gives the double-layer protection that
AUTH_TEST_PLAN test 7.5.9 documents:

  Layer 1 (AuthMiddleware): cookie + JWT validation, rejects junk
                            cookies and stamps request.state.user
  Layer 2 (@require_permission with owner_check=True): per-resource
                            ownership verification via
                            ThreadMetaStore.check_access — returns
                            404 if a different user owns the thread

The decorator's owner_check branch is rewritten to use the SQL
thread_meta_repo (the 2.0-rc persistence layer) instead of the
LangGraph store path that PR #1728 used (_store_get / get_store
in routers/threads.py). The inject_record convenience is dropped
— no caller in 2.0 needs the LangGraph blob, and the SQL repo has
a different shape.

Routes decorated (28 total):
- threads.py: delete, patch, get, get-state, post-state, post-history
- thread_runs.py: post-runs, post-runs-stream, post-runs-wait,
  list_runs, get_run, cancel_run, join_run, stream_existing_run,
  list_thread_messages, list_run_messages, list_run_events,
  thread_token_usage
- feedback.py: create, list, stats, delete
- uploads.py: upload (added Request param), list, delete
- artifacts.py: get_artifact
- suggestions.py: generate (renamed body parameter to avoid
  conflict with FastAPI Request)

Test fixes:
- test_suggestions_router.py: bypass the decorator via __wrapped__
  (the unit tests cover parsing logic, not auth — no point spinning
  up a thread_meta_repo just to test JSON unwrapping)
- test_auth_middleware.py 4 fake-cookie tests: already updated in
  the previous commit (745bf432)

Tests: 293 passed (auth + persistence + isolation + suggestions)
Lint: clean

* security(auth): defense-in-depth fixes from release validation pass

Eight findings caught while running the AUTH_TEST_PLAN end-to-end against
the deployed sg_dev stack. Each is a pre-condition for shipping
release/2.0-rc that the previous PRs missed.

Backend hardening
- routers/auth.py: rate limiter X-Real-IP now requires AUTH_TRUSTED_PROXIES
  whitelist (CIDR/IP allowlist). Without nginx in front, the previous code
  honored arbitrary X-Real-IP, letting an attacker rotate the header to
  fully bypass the per-IP login lockout.
- routers/auth.py: 36-entry common-password blocklist via Pydantic
  field_validator on RegisterRequest + ChangePasswordRequest. The shared
  _validate_strong_password helper keeps the constraint in one place.
- routers/threads.py: ThreadCreateRequest + ThreadPatchRequest strip
  server-reserved metadata keys (owner_id, user_id) via Pydantic
  field_validator so a forged value can never round-trip back to other
  clients reading the same thread. The actual ownership invariant stays
  on the threads_meta row; this closes the metadata-blob echo gap.
- authz.py + thread_meta/sql.py: require_permission gains a require_existing
  flag plumbed through check_access(require_existing=True). Destructive
  routes (DELETE/PATCH/state-update/runs/feedback) now treat a missing
  thread_meta row as 404 instead of "untracked legacy thread, allow",
  closing the cross-user delete-idempotence gap where any user could
  successfully DELETE another user's deleted thread.
- repositories/sqlite.py + base.py: update_user raises UserNotFoundError
  on a vanished row instead of silently returning the input. Concurrent
  delete during password reset can no longer look like a successful update.
- runtime/user_context.py: resolve_owner_id() coerces User.id (UUID) to
  str at the contextvar boundary so SQLAlchemy String(64) columns can
  bind it. The whole 2.0-rc isolation pipeline was previously broken
  end-to-end (POST /api/threads → 500 "type 'UUID' is not supported").
- persistence/engine.py: SQLAlchemy listener enables PRAGMA journal_mode=WAL,
  synchronous=NORMAL, foreign_keys=ON on every new SQLite connection.
  TC-UPG-06 in the test plan expects WAL; previous code shipped with the
  default 'delete' journal.
- auth_middleware.py: stamp request.state.auth = AuthContext(...) so
  @require_permission's short-circuit fires; previously every isolation
  request did a duplicate JWT decode + users SELECT. Also unifies the
  401 payload through AuthErrorResponse(...).model_dump().
- app.py: _ensure_admin_user restructure removes the noqa F821 scoping
  bug where 'password' was referenced outside the branch that defined it.
  New _announce_credentials helper absorbs the duplicate log block in
  the fresh-admin and reset-admin branches.

* fix(frontend+nginx): rollout CSRF on every state-changing client path

The frontend was 100% broken in gateway-pro mode for any user trying to
open a specific chat thread. Three cumulative bugs each silently
masked the next.

LangGraph SDK CSRF gap (api-client.ts)
- The Client constructor took only apiUrl, no defaultHeaders, no fetch
  interceptor. The SDK's internal fetch never sent X-CSRF-Token, so
  every state-changing /api/langgraph-compat/* call (runs/stream,
  threads/search, threads/{tid}/history, ...) hit CSRFMiddleware and
  got 403 before reaching the auth check. UI symptom: empty thread page
  with no error message; the SPA's hooks swallowed the rejection.
- Fix: pass an onRequest hook that injects X-CSRF-Token from the
  csrf_token cookie per request. Reading the cookie per call (not at
  construction time) handles login / logout / password-change cookie
  rotation transparently. The SDK's prepareFetchOptions calls
  onRequest for both regular requests AND streaming/SSE/reconnect, so
  the same hook covers runs.stream and runs.joinStream.

Raw fetch CSRF gap (7 files)
- Audit: 11 frontend fetch sites, only 2 included CSRF (login/setup +
  account-settings change-password). The other 7 routed through raw
  fetch() with no header — suggestions, memory, agents, mcp, skills,
  uploads, and the local thread cleanup hook all 403'd silently.
- Fix: enhance fetcher.ts:fetchWithAuth to auto-inject X-CSRF-Token on
  POST/PUT/DELETE/PATCH from a single shared readCsrfCookie() helper.
  Convert all 7 raw fetch() callers to fetchWithAuth so the contract
  is centrally enforced. api-client.ts and fetcher.ts share
  readCsrfCookie + STATE_CHANGING_METHODS to avoid drift.

nginx routing + buffering (nginx.local.conf)
- The auth feature shipped without updating the nginx config: per-API
  explicit location blocks but no /api/v1/auth/, /api/feedback, /api/runs.
  The frontend's client-side fetches to /api/v1/auth/login/local 404'd
  from the Next.js side because nginx routed /api/* to the frontend.
- Fix: add catch-all `location /api/` that proxies to the gateway.
  nginx longest-prefix matching keeps the explicit blocks (/api/models,
  /api/threads regex, /api/langgraph/, ...) winning for their paths.
- Fix: disable proxy_buffering + proxy_request_buffering for the
  frontend `location /` block. Without it, nginx tries to spool large
  Next.js chunks into /var/lib/nginx/proxy (root-owned) and fails with
  Permission denied → ERR_INCOMPLETE_CHUNKED_ENCODING → ChunkLoadError.

* test(auth): release-validation test infra and new coverage

Test fixtures and unit tests added during the validation pass.

Router test helpers (NEW: tests/_router_auth_helpers.py)
- make_authed_test_app(): builds a FastAPI test app with a stub
  middleware that stamps request.state.user + request.state.auth and a
  permissive thread_meta_repo mock. TestClient-based router tests
  (test_artifacts_router, test_threads_router) use it instead of bare
  FastAPI() so the new @require_permission(owner_check=True) decorators
  short-circuit cleanly.
- call_unwrapped(): walks the __wrapped__ chain to invoke the underlying
  handler without going through the authz wrappers. Direct-call tests
  (test_uploads_router) use it. Typed with ParamSpec so the wrapped
  signature flows through.

Backend test additions
- test_auth.py: 7 tests for the new _get_client_ip trust model (no
  proxy / trusted proxy / untrusted peer / XFF rejection / invalid
  CIDR / no client). 5 tests for the password blocklist (literal,
  case-insensitive, strong password accepted, change-password binding,
  short-password length-check still fires before blocklist).
  test_update_user_raises_when_row_concurrently_deleted: closes a
  shipped-without-coverage gap on the new UserNotFoundError contract.
- test_thread_meta_repo.py: 4 tests for check_access(require_existing=True)
  — strict missing-row denial, strict owner match, strict owner mismatch,
  strict null-owner still allowed (shared rows survive the tightening).
- test_ensure_admin.py: 3 tests for _migrate_orphaned_threads /
  _iter_store_items pagination, covering the TC-UPG-02 upgrade story
  end-to-end via mock store. Closes the gap where the cursor pagination
  was untested even though the previous PR rewrote it.
- test_threads_router.py: 5 tests for _strip_reserved_metadata
  (owner_id removal, user_id removal, safe-keys passthrough, empty
  input, both-stripped).
- test_auth_type_system.py: replace "password123" fixtures with
  Tr0ub4dor3a / AnotherStr0ngPwd! so the new password blocklist
  doesn't reject the test data.

* docs(auth): refresh TC-DOCKER-05 + document Docker validation gap

- AUTH_TEST_PLAN.md TC-DOCKER-05: the previous expectation
  ("admin password visible in docker logs") was stale after the simplify
  pass that moved credentials to a 0600 file. The grep "Password:" check
  would have silently failed and given a false sense of coverage. New
  expectation matches the actual file-based path: 0600 file in
  DEER_FLOW_HOME, log shows the path (not the secret), reverse-grep
  asserts no leaked password in container logs.
- NEW: docs/AUTH_TEST_DOCKER_GAP.md documents the only un-executed
  block in the test plan (TC-DOCKER-01..06). Reason: sg_dev validation
  host has no Docker daemon installed. The doc maps each Docker case
  to an already-validated bare-metal equivalent (TC-1.1, TC-REENT-01,
  TC-API-02 etc.) so the gap is auditable, and includes pre-flight
  reproduction steps for whoever has Docker available.

---------

Co-authored-by: greatmengqi <chenmengqi.0376@bytedance.com>

* refactor(persistence): unify SQLite to single deerflow.db and move checkpointer to runtime

Merge checkpoints.db and app.db into a single deerflow.db file (WAL mode
handles concurrent access safely). Move checkpointer module from
agents/checkpointer to runtime/checkpointer to better reflect its role
as a runtime infrastructure concern.

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

* refactor(persistence): rename owner_id to user_id and thread_meta_repo to thread_store

Rename owner_id to user_id across all persistence models, repositories,
stores, routers, and tests for clearer semantics. Rename thread_meta_repo
to thread_store for consistency with run_store/run_event_store naming.
Add ThreadMetaStore return type annotation to get_thread_store().

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

* feat(persistence): unify ThreadMetaStore interface with user isolation and factory

Add user_id parameter to all ThreadMetaStore abstract methods. Implement
owner isolation in MemoryThreadMetaStore with _get_owned_record helper.
Add check_access to base class and memory implementation. Add
make_thread_store factory to simplify deps.py initialization. Add
memory-backend isolation tests.

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

* feat(feedback): add UNIQUE(thread_id, run_id, user_id) constraint

Add UNIQUE constraint to FeedbackRow to enforce one feedback per user per run,
enabling upsert behavior in Task 2. Update tests to use distinct user_ids for
multiple feedback records per run, and pass user_id=None to list_by_run for
admin-style queries that bypass user isolation.

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

* feat(feedback): add upsert() method with UNIQUE enforcement

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

* feat(feedback): add delete_by_run() and list_by_thread_grouped()

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

* feat(feedback): add PUT upsert and DELETE-by-run endpoints

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

* feat(feedback): enrich messages endpoint with per-run feedback data

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

* feat(feedback): add frontend feedback API client

Adds upsertFeedback and deleteFeedback API functions backed by
fetchWithAuth, targeting the /api/threads/{id}/runs/{id}/feedback
endpoint.

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

* feat(feedback): wire feedback data into message rendering for history echo

Adds useThreadFeedback hook that fetches run-level feedback from the
messages API and builds a runId->FeedbackData map. MessageList now calls
this hook and passes feedback and runId to each MessageListItem so
previously-submitted thumbs are pre-filled when revisiting a thread.

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

* fix(feedback): correct run_id mapping for feedback echo

The feedbackMap was keyed by run_id but looked up by LangGraph message ID.
Fixed by tracking AI message ordinal index to correlate event store
run_ids with LangGraph SDK messages.

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

* fix(feedback): use real threadId and refresh after stream

- Pass threadId prop to MessageListItem instead of reading "new" from URL params
- Invalidate thread-feedback query on stream finish so buttons appear immediately
- Show feedback buttons always visible, copy button on hover only

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

* style(feedback): group copy and feedback buttons together on the left

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

* style(feedback): always show toolbar buttons without hover

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

* fix(persistence): stream hang when run_events.backend=db

DbRunEventStore._user_id_from_context() returned user.id without
coercing it to str. User.id is a Pydantic UUID, and aiosqlite cannot
bind a raw UUID object to a VARCHAR column, so the INSERT for the
initial human_message event silently rolled back and raised out of
the worker task. Because that put() sat outside the worker's try
block, the finally-clause that publishes end-of-stream never ran
and the SSE stream hung forever.

jsonl mode was unaffected because json.dumps(default=str) coerces
UUID objects transparently.

Fixes:
- db.py: coerce user.id to str at the context-read boundary (matches
  what resolve_user_id already does for the other repositories)
- worker.py: move RunJournal init + human_message put inside the try
  block so any failure flows through the finally/publish_end path
  instead of hanging the subscriber

Defense-in-depth:
- engine.py: add PRAGMA busy_timeout=5000 so checkpointer and event
  store wait for each other on the shared deerflow.db file instead
  of failing immediately under write-lock contention
- journal.py: skip fire-and-forget _flush_sync when a previous flush
  task is still in flight, to avoid piling up concurrent put_batch
  writes on the same SQLAlchemy engine during streaming; flush() now
  waits for pending tasks before draining the buffer
- database_config.py: doc-only update clarifying WAL + busy_timeout
  keep the unified deerflow.db safe for both workloads

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

* chore(persistence): drop redundant busy_timeout PRAGMA

Python's sqlite3 driver defaults to a 5-second busy timeout via the
``timeout`` kwarg of ``sqlite3.connect``, and aiosqlite + SQLAlchemy's
aiosqlite dialect inherit that default. Setting ``PRAGMA busy_timeout=5000``
explicitly was a no-op — verified by reading back the PRAGMA on a fresh
connection (it already reports 5000ms without our PRAGMA).

Concurrent stress test (50 checkpoint writes + 20 event batches + 50
thread_meta updates on the same deerflow.db) still completes with zero
errors and 200/200 rows after removing the explicit PRAGMA.

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

* fix(journal): unwrap Command tool results in on_tool_end

Tools that update graph state (e.g. ``present_files``) return
``Command(update={'messages': [ToolMessage(...)], 'artifacts': [...]})``.
LangGraph later unwraps the inner ``ToolMessage`` into checkpoint state,
but ``RunJournal.on_tool_end`` was receiving the ``Command`` object
directly via the LangChain callback chain and storing
``str(Command(update={...}))`` as the tool_result content.

This produced a visible divergence between the event-store and the
checkpoint for any thread that used a Command-returning tool, blocking
the event-store-backed history fix in the follow-up commit. Concrete
example from thread ``6d30913e-dcd4-41c8-8941-f66c716cf359`` (seq=48):
checkpoint had ``'Successfully presented files'`` while event_store
stored the full Command repr.

The fix detects ``Command`` in ``on_tool_end``, extracts the first
``ToolMessage`` from ``update['messages']``, and lets the existing
ToolMessage branch handle the ``model_dump()`` path. Legacy rows still
containing the Command repr are separately cleaned up by the history
helper in the follow-up commit.

Tests:
- ``test_tool_end_unwraps_command_with_inner_tool_message`` — unit test
  of the unwrap branch with a constructed Command
- ``test_tool_invoke_end_to_end_unwraps_command`` — end-to-end via
  ``CallbackManager`` + ``tool.invoke`` to exercise the real LangChain
  dispatch path that production uses, matching the repro shape from
  ``present_files``
- Counter-proof: temporarily reverted the patch, both tests failed with
  the exact ``Command(update={...})`` repr that was stored in the
  production SQLite row at seq=48, confirming LangChain does pass the
  ``Command`` through callbacks (the unwrap is load-bearing)

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

* fix(threads): load history messages from event store, immune to summarize

``get_thread_history`` and ``get_thread_state`` in Gateway mode read
messages from ``checkpoint.channel_values["messages"]``. After
SummarizationMiddleware runs mid-run, that list is rewritten in-place:
pre-summarize messages are dropped and a synthetic summary-as-human
message takes position 0. The frontend then renders a chat history that
starts with ``"Here is a summary of the conversation to date:..."``
instead of the user's original query, and all earlier turns are gone.

The event store (``RunEventStore``) is append-only and never rewritten,
so it retains the full transcript. This commit adds a helper
``_get_event_store_messages`` that loads the event store's message
stream and overrides ``values["messages"]`` in both endpoints; the
checkpoint fallback kicks in only when the event store is unavailable.

Behavior contract of the helper:

- **Full pagination.** ``list_messages`` returns the newest ``limit``
  records when no cursor is given, so a fixed limit silently drops
  older messages on long threads. The helper sizes the read from
  ``count_messages()`` and pages forward with ``after_seq`` cursors.
- **Copy-on-read.** Each content dict is copied before ``id`` is
  patched so the live store object (``MemoryRunEventStore`` returns
  references) is never mutated.
- **Stable ids.** Messages with ``id=None`` (human + tool_result,
  which don't receive an id until checkpoint persistence) get a
  deterministic ``uuid5(NAMESPACE_URL, f"{thread_id}:{seq}")`` so
  React keys stay stable across requests. AI messages keep their
  LLM-assigned ``lc_run--*`` ids.
- **Legacy ``Command`` repr sanitization.** Rows captured before the
  ``journal.py`` ``on_tool_end`` fix (previous commit) stored
  ``str(Command(update={'messages': [ToolMessage(content='X', ...)]}))``
  as the tool_result content. ``_sanitize_legacy_command_repr``
  regex-extracts the inner text so old threads render cleanly.
- **Inline feedback.** When loading the stream, the helper also pulls
  ``feedback_repo.list_by_thread_grouped`` and attaches ``run_id`` to
  every message plus ``feedback`` to the final ``ai_message`` of each
  run. This removes the frontend's need to fetch a second endpoint
  and positional-index-map its way back to the right run. When the
  feedback subsystem is unavailable, the ``feedback`` field is left
  absent entirely so the frontend hides the button rather than
  rendering it over a broken write path.
- **User context.** ``DbRunEventStore`` is user-scoped by default via
  ``resolve_user_id(AUTO)``. The helper relies on the ``@require_permission``
  decorator having populated the user contextvar on both callers; the
  docstring documents this dependency explicitly so nobody wires it
  into a CLI or migration script without passing ``user_id=None``.

Real data verification against thread
``6d30913e-dcd4-41c8-8941-f66c716cf359``: checkpoint showed 12 messages
(summarize-corrupted), event store had 16. The original human message
``"最新伊美局势"`` was preserved as seq=1 in the event store and
correctly restored to position 0 in the helper output. Helper output
for AI messages was byte-identical to checkpoint for every overlapping
message; only tool_result ids differed (patched to uuid5) and the
legacy Command repr at seq=48 was sanitized.

Tests:
- ``test_thread_state_event_store.py`` — 18 tests covering
  ``_sanitize_legacy_command_repr`` (passthrough, single/double-quote
  extraction, unparseable fallback), helper happy path (all message
  types, stable uuid5, store non-mutation), multi-page pagination,
  summarize regression (recovers pre-summarize messages), feedback
  attachment (per-run, multi-run threads, repo failure graceful),
  and dependency failure fallback to ``None``.

Docs:
- ``docs/superpowers/plans/2026-04-10-event-store-history.md`` — the
  implementation plan this commit realizes, with Task 1 revised after
  the evaluation findings (pagination, copy-on-read, Command wrap
  already landed in journal.py, frontend feedback pagination in the
  follow-up commit, Standard-mode follow-up noted).
- ``docs/superpowers/specs/2026-04-11-runjournal-history-evaluation.md``
  — the Claude + second-opinion evaluation document that drove the
  plan revisions (pagination bug, dict-mutation bug, feedback hidden
  bug, Command bug).
- ``docs/superpowers/specs/2026-04-11-summarize-marker-design.md`` —
  design for a follow-up PR that visually marks summarize events in
  history, based on a verified ``adispatch_custom_event`` experiment
  (``trace=False`` middleware nodes can still forward the Pregel task
  config via explicit signature injection).

Scope: Gateway mode only (``make dev-pro``). Standard mode
(``make dev``) hits LangGraph Server directly and bypasses these
endpoints; the summarize symptom is still present there and is
tracked as a separate follow-up in the plan.

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

* refactor(feedback): inline feedback on history and drop positional mapping

The old ``useThreadFeedback`` hook loaded ``GET /api/threads/{id}/messages?limit=200``
and built two parallel lookup tables: ``runIdByAiIndex`` (an ordinal array of
run_ids for every ``ai_message``-typed event) and ``feedbackByRunId``. The render
loop in ``message-list.tsx`` walked the AI messages in order, incrementing
``aiMessageIndex`` on each non-human message, and used that ordinal to look up
the run_id and feedback.

This shape had three latent bugs we could observe on real threads:

1. **Fetch was capped at 200 messages.** Long or tool-heavy threads silently
   dropped earlier entries from the map, so feedback buttons could be missing
   on messages they should own.
2. **Ordinal mismatch.** The render loop counted every non-human message
   (including each intermediate ``ai_tool_call``), but ``runIdByAiIndex`` only
   pushed entries for ``event_type == "ai_message"``. A run with 3 tool_calls
   + 1 final AI message would push 1 entry while the render consumed 4
   positions, so buttons mapped to the wrong positions across multi-run
   threads.
3. **Two parallel data paths.** The ``/history`` render path and the
   ``/messages`` feedback-lookup path could drift in-between an
   ``invalidateQueries`` call and the next refetch, producing transient
   mismaps.

The previous commit moved the authoritative message source for history to
the event store and added ``run_id`` + ``feedback`` inline on each message
dict returned by ``_get_event_store_messages``. This commit aligns the
frontend with that contract:

- **Delete** ``useThreadFeedback``, ``ThreadFeedbackData``,
  ``runIdByAiIndex``, ``feedbackByRunId``, and ``fetchAllThreadMessages``.
- **Introduce** ``useThreadMessageEnrichment`` that fetches
  ``POST /history?limit=1`` once, indexes the returned messages by
  ``message.id`` into a ``Map<id, {run_id, feedback?}>``, and invalidates
  on stream completion (``onFinish`` in ``useThreadStream``). Keying by
  ``message.id`` is stable across runs, tool_call chains, and summarize.
- **Simplify** ``message-list.tsx`` to drop the ``aiMessageIndex``
  counter and read ``enrichment?.get(msg.id)`` at each render step.
- **Rewire** ``message-list-item.tsx`` so the feedback button renders
  when ``feedback !== undefined`` rather than when the message happens
  to be non-human. ``feedback`` is ``undefined`` for non-eligible
  messages (humans, non-final AI, tools), ``null`` for the final
  ai_message of an unrated run, and a ``FeedbackData`` object once
  rated — cleanly distinguishing "not eligible" from "eligible but
  unrated".

``/api/threads/{id}/messages`` is kept as a debug/export surface; no
frontend code calls it anymore but the backend router is untouched.

Validation:
- ``pnpm check`` clean (0 errors, 1 pre-existing unrelated warning)
- Live test on thread ``3d5dea4a`` after gateway restart confirmed the
  original user query is restored to position 0 and the feedback
  button behaves correctly on the final AI message.

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

* 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>

* fix(rebase): restore FeedbackButtons component and enrichment lost during rebase

The FeedbackButtons component (defined inline in message-list-item.tsx)
was introduced in commit 95df8d13 but lost during rebase. The previous
rebase cleanup commit incorrectly removed the feedback/runId props and
enrichment hook as "orphaned code" instead of restoring the missing
component. This commit restores:

- FeedbackButtons component with thumbs up/down toggle and optimistic state
- FeedbackData/upsertFeedback/deleteFeedback imports
- feedback and runId props on MessageListItem
- useThreadMessageEnrichment hook and entry lookup in message-list.tsx

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

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
Co-authored-by: DanielWalnut <45447813+hetaoBackend@users.noreply.github.com>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Co-authored-by: JilongSun <965640067@qq.com>
Co-authored-by: jie <49781832+stan-fu@users.noreply.github.com>
Co-authored-by: cooper <cooperfu@tencent.com>
Co-authored-by: yangzheli <43645580+yangzheli@users.noreply.github.com>
Co-authored-by: greatmengqi <chenmengqi.0376@gmail.com>
Co-authored-by: greatmengqi <chenmengqi.0376@bytedance.com>

backend/app/gateway/app.py

@@ -42,6 +42,11 @@ logger = logging.getLogger(__name__)
 async def _ensure_admin_user(app: FastAPI) -> None:
     """Startup hook: generate init token on first boot; migrate orphan threads otherwise.
 
+    After admin creation, migrate orphan threads from the LangGraph
+    store (metadata.user_id unset) to the admin account. This is the
+    "no-auth → with-auth" upgrade path: users who ran DeerFlow without
+    authentication have existing LangGraph thread data that needs an
+    owner assigned.
     First boot (no admin exists):
       - Generates a one-time ``init_token`` stored in ``app.state.init_token``
       - Logs the token to stdout so the operator can copy-paste it into the
@@ -52,7 +57,7 @@ async def _ensure_admin_user(app: FastAPI) -> None:
       - Runs the one-time "no-auth → with-auth" orphan thread migration for
         existing LangGraph thread metadata that has no owner_id.
 
-    No SQL persistence migration is needed: the four owner_id columns
+    No SQL persistence migration is needed: the four user_id columns
     (threads_meta, runs, run_events, feedback) only come into existence
     alongside the auth module via create_all, so freshly created tables
     never contain NULL-owner rows.
@@ -96,6 +101,8 @@ async def _ensure_admin_user(app: FastAPI) -> None:
     admin_id = str(row.id)
 
     # LangGraph store orphan migration — non-fatal.
+    # This covers the "no-auth → with-auth" upgrade path for users
+    # whose existing LangGraph thread metadata has no user_id set.
     store = getattr(app.state, "store", None)
     if store is not None:
         try:
@@ -127,7 +134,7 @@ async def _iter_store_items(store, namespace, *, page_size: int = 500):
 
 
 async def _migrate_orphaned_threads(store, admin_user_id: str) -> int:
-    """Migrate LangGraph store threads with no owner_id to the given admin.
+    """Migrate LangGraph store threads with no user_id to the given admin.
 
     Uses cursor pagination so all orphans are migrated regardless of
     count. Returns the number of rows migrated.
@@ -135,8 +142,8 @@ async def _migrate_orphaned_threads(store, admin_user_id: str) -> int:
     migrated = 0
     async for item in _iter_store_items(store, ("threads",)):
         metadata = item.value.get("metadata", {})
-        if not metadata.get("owner_id"):
-            metadata["owner_id"] = admin_user_id
+        if not metadata.get("user_id"):
+            metadata["user_id"] = admin_user_id
             item.value["metadata"] = metadata
             await store.aput(("threads",), item.key, item.value)
             migrated += 1

backend/app/gateway/authz.py

@@ -233,18 +233,18 @@ def require_permission(
             # (``threads_meta`` table). We verify ownership via
             # ``ThreadMetaStore.check_access``: it returns True for
             # missing rows (untracked legacy thread) and for rows whose
-            # ``owner_id`` is NULL (shared / pre-auth data), so this is
+            # ``user_id`` is NULL (shared / pre-auth data), so this is
             # strict-deny rather than strict-allow — only an *existing*
-            # row with a *different* owner_id triggers 404.
+            # row with a *different* user_id triggers 404.
             if owner_check:
                 thread_id = kwargs.get("thread_id")
                 if thread_id is None:
                     raise ValueError("require_permission with owner_check=True requires 'thread_id' parameter")
 
-                from app.gateway.deps import get_thread_meta_repo
+                from app.gateway.deps import get_thread_store
 
-                thread_meta_repo = get_thread_meta_repo(request)
-                allowed = await thread_meta_repo.check_access(
+                thread_store = get_thread_store(request)
+                allowed = await thread_store.check_access(
                     thread_id,
                     str(auth.user.id),
                     require_existing=require_existing,

backend/app/gateway/deps.py

@@ -1,8 +1,7 @@
 """Centralized accessors for singleton objects stored on ``app.state``.
 
 **Getters** (used by routers): raise 503 when a required dependency is
-missing, except ``get_store`` and ``get_thread_meta_repo`` which return
-``None``.
+missing, except ``get_store`` which returns ``None``.
 
 Initialization is handled directly in ``app.py`` via :class:`AsyncExitStack`.
 """
@@ -20,6 +19,7 @@ from deerflow.runtime import RunContext, RunManager
 if TYPE_CHECKING:
     from app.gateway.auth.local_provider import LocalAuthProvider
     from app.gateway.auth.repositories.sqlite import SQLiteUserRepository
+    from deerflow.persistence.thread_meta.base import ThreadMetaStore
 
 
 @asynccontextmanager
@@ -31,10 +31,10 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
         async with langgraph_runtime(app):
             yield
     """
-    from deerflow.agents.checkpointer.async_provider import make_checkpointer
     from deerflow.config import get_app_config
     from deerflow.persistence.engine import close_engine, get_session_factory, init_engine_from_config
     from deerflow.runtime import make_store, make_stream_bridge
+    from deerflow.runtime.checkpointer.async_provider import make_checkpointer
     from deerflow.runtime.events.store import make_run_event_store
 
     async with AsyncExitStack() as stack:
@@ -53,18 +53,18 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
         if sf is not None:
             from deerflow.persistence.feedback import FeedbackRepository
             from deerflow.persistence.run import RunRepository
-            from deerflow.persistence.thread_meta import ThreadMetaRepository
 
             app.state.run_store = RunRepository(sf)
             app.state.feedback_repo = FeedbackRepository(sf)
-            app.state.thread_meta_repo = ThreadMetaRepository(sf)
         else:
-            from deerflow.persistence.thread_meta import MemoryThreadMetaStore
             from deerflow.runtime.runs.store.memory import MemoryRunStore
 
             app.state.run_store = MemoryRunStore()
             app.state.feedback_repo = None
-            app.state.thread_meta_repo = MemoryThreadMetaStore(app.state.store)
+
+        from deerflow.persistence.thread_meta import make_thread_store
+
+        app.state.thread_store = make_thread_store(sf, app.state.store)
 
         # Run event store (has its own factory with config-driven backend selection)
         run_events_config = getattr(config, "run_events", None)
@@ -80,7 +80,7 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
 
 
 # ---------------------------------------------------------------------------
-# Getters -- called by routers per-request
+# Getters – called by routers per-request
 # ---------------------------------------------------------------------------
 
 
@@ -110,7 +110,12 @@ def get_store(request: Request):
     return getattr(request.app.state, "store", None)
 
 
-get_thread_meta_repo = _require("thread_meta_repo", "Thread metadata store")
+def get_thread_store(request: Request) -> ThreadMetaStore:
+    """Return the thread metadata store (SQL or memory-backed)."""
+    val = getattr(request.app.state, "thread_store", None)
+    if val is None:
+        raise HTTPException(status_code=503, detail="Thread metadata store not available")
+    return val
 
 
 def get_run_context(request: Request) -> RunContext:
@@ -128,10 +133,11 @@ def get_run_context(request: Request) -> RunContext:
         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),
+        thread_store=get_thread_store(request),
     )
 
 
+
 # ---------------------------------------------------------------------------
 # Auth helpers (used by authz.py and auth middleware)
 # ---------------------------------------------------------------------------

backend/app/gateway/langgraph_auth.py

@@ -93,14 +93,14 @@ async def authenticate(request):
 
 @auth.on
 async def add_owner_filter(ctx: Auth.types.AuthContext, value: dict):
-    """Inject owner_id metadata on writes; filter by owner_id on reads.
+    """Inject user_id metadata on writes; filter by user_id on reads.
 
-    Gateway stores thread ownership as ``metadata.owner_id``.
+    Gateway stores thread ownership as ``metadata.user_id``.
     This handler ensures LangGraph Server enforces the same isolation.
     """
-    # On create/update: stamp owner_id into metadata
+    # On create/update: stamp user_id into metadata
     metadata = value.setdefault("metadata", {})
-    metadata["owner_id"] = ctx.user.identity
+    metadata["user_id"] = ctx.user.identity
 
     # Return filter dict — LangGraph applies it to search/read/delete
-    return {"owner_id": ctx.user.identity}
+    return {"user_id": ctx.user.identity}

backend/app/gateway/routers/feedback.py

@@ -30,11 +30,16 @@ class FeedbackCreateRequest(BaseModel):
     message_id: str | None = Field(default=None, description="Optional: scope feedback to a specific message")
 
 
+class FeedbackUpsertRequest(BaseModel):
+    rating: int = Field(..., description="Feedback rating: +1 (positive) or -1 (negative)")
+    comment: str | None = Field(default=None, description="Optional text feedback")
+
+
 class FeedbackResponse(BaseModel):
     feedback_id: str
     run_id: str
     thread_id: str
-    owner_id: str | None = None
+    user_id: str | None = None
     message_id: str | None = None
     rating: int
     comment: str | None = None
@@ -53,6 +58,57 @@ class FeedbackStatsResponse(BaseModel):
 # ---------------------------------------------------------------------------
 
 
+@router.put("/{thread_id}/runs/{run_id}/feedback", response_model=FeedbackResponse)
+@require_permission("threads", "write", owner_check=True, require_existing=True)
+async def upsert_feedback(
+    thread_id: str,
+    run_id: str,
+    body: FeedbackUpsertRequest,
+    request: Request,
+) -> dict[str, Any]:
+    """Create or update feedback for a run (idempotent)."""
+    if body.rating not in (1, -1):
+        raise HTTPException(status_code=400, detail="rating must be +1 or -1")
+
+    user_id = await get_current_user(request)
+
+    run_store = get_run_store(request)
+    run = await run_store.get(run_id)
+    if run is None:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found")
+    if run.get("thread_id") != thread_id:
+        raise HTTPException(status_code=404, detail=f"Run {run_id} not found in thread {thread_id}")
+
+    feedback_repo = get_feedback_repo(request)
+    return await feedback_repo.upsert(
+        run_id=run_id,
+        thread_id=thread_id,
+        rating=body.rating,
+        user_id=user_id,
+        comment=body.comment,
+    )
+
+
+@router.delete("/{thread_id}/runs/{run_id}/feedback")
+@require_permission("threads", "delete", owner_check=True, require_existing=True)
+async def delete_run_feedback(
+    thread_id: str,
+    run_id: str,
+    request: Request,
+) -> dict[str, bool]:
+    """Delete the current user's feedback for a run."""
+    user_id = await get_current_user(request)
+    feedback_repo = get_feedback_repo(request)
+    deleted = await feedback_repo.delete_by_run(
+        thread_id=thread_id,
+        run_id=run_id,
+        user_id=user_id,
+    )
+    if not deleted:
+        raise HTTPException(status_code=404, detail="No feedback found for this run")
+    return {"success": True}
+
+
 @router.post("/{thread_id}/runs/{run_id}/feedback", response_model=FeedbackResponse)
 @require_permission("threads", "write", owner_check=True, require_existing=True)
 async def create_feedback(
@@ -80,7 +136,7 @@ async def create_feedback(
         run_id=run_id,
         thread_id=thread_id,
         rating=body.rating,
-        owner_id=user_id,
+        user_id=user_id,
         message_id=body.message_id,
         comment=body.comment,
     )

backend/app/gateway/routers/thread_runs.py

@@ -20,7 +20,7 @@ from fastapi.responses import Response, StreamingResponse
 from pydantic import BaseModel, Field
 
 from app.gateway.authz import require_permission
-from app.gateway.deps import get_checkpointer, get_run_event_store, get_run_manager, get_run_store, get_stream_bridge
+from app.gateway.deps import get_checkpointer, get_current_user, get_feedback_repo, get_run_event_store, get_run_manager, get_run_store, get_stream_bridge
 from app.gateway.services import sse_consumer, start_run
 from deerflow.runtime import RunRecord, serialize_channel_values
 
@@ -291,9 +291,36 @@ async def list_thread_messages(
     before_seq: int | None = Query(default=None),
     after_seq: int | None = Query(default=None),
 ) -> list[dict]:
-    """Return displayable messages for a thread (across all runs)."""
+    """Return displayable messages for a thread (across all runs), with feedback attached."""
     event_store = get_run_event_store(request)
-    return await event_store.list_messages(thread_id, limit=limit, before_seq=before_seq, after_seq=after_seq)
+    messages = await event_store.list_messages(thread_id, limit=limit, before_seq=before_seq, after_seq=after_seq)
+
+    # Attach feedback to the last AI message of each run
+    feedback_repo = get_feedback_repo(request)
+    user_id = await get_current_user(request)
+    feedback_map = await feedback_repo.list_by_thread_grouped(thread_id, user_id=user_id)
+
+    # Find the last ai_message per run_id
+    last_ai_per_run: dict[str, int] = {}  # run_id -> index in messages list
+    for i, msg in enumerate(messages):
+        if msg.get("event_type") == "ai_message":
+            last_ai_per_run[msg["run_id"]] = i
+
+    # Attach feedback field
+    last_ai_indices = set(last_ai_per_run.values())
+    for i, msg in enumerate(messages):
+        if i in last_ai_indices:
+            run_id = msg["run_id"]
+            fb = feedback_map.get(run_id)
+            msg["feedback"] = {
+                "feedback_id": fb["feedback_id"],
+                "rating": fb["rating"],
+                "comment": fb.get("comment"),
+            } if fb else None
+        else:
+            msg["feedback"] = None
+
+    return messages
 
 
 @router.get("/{thread_id}/runs/{run_id}/messages")

backend/app/gateway/routers/threads.py

@@ -13,6 +13,7 @@ matching the LangGraph Platform wire format expected by the
 from __future__ import annotations
 
 import logging
+import re
 import time
 import uuid
 from typing import Any
@@ -21,7 +22,7 @@ from fastapi import APIRouter, HTTPException, Request
 from pydantic import BaseModel, Field, field_validator
 
 from app.gateway.authz import require_permission
-from app.gateway.deps import get_checkpointer
+from app.gateway.deps import get_checkpointer, get_current_user, get_feedback_repo, get_run_event_store
 from app.gateway.utils import sanitize_log_param
 from deerflow.config.paths import Paths, get_paths
 from deerflow.runtime import serialize_channel_values
@@ -34,7 +35,7 @@ router = APIRouter(prefix="/api/threads", tags=["threads"])
 # them. Pydantic ``@field_validator("metadata")`` strips them on every
 # inbound model below so a malicious client cannot reflect a forged
 # owner identity through the API surface. Defense-in-depth — the
-# row-level invariant is still ``threads_meta.owner_id`` populated from
+# row-level invariant is still ``threads_meta.user_id`` populated from
 # the auth contextvar; this list closes the metadata-blob echo gap.
 _SERVER_RESERVED_METADATA_KEYS: frozenset[str] = frozenset({"owner_id", "user_id"})
 
@@ -194,7 +195,7 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
     and removes the thread_meta row from the configured ThreadMetaStore
     (sqlite or memory).
     """
-    from app.gateway.deps import get_thread_meta_repo
+    from app.gateway.deps import get_thread_store
 
     # Clean local filesystem
     response = _delete_thread_data(thread_id)
@@ -211,8 +212,8 @@ async def delete_thread_data(thread_id: str, request: Request) -> ThreadDeleteRe
     # Remove thread_meta row (best-effort) — required for sqlite backend
     # so the deleted thread no longer appears in /threads/search.
     try:
-        thread_meta_repo = get_thread_meta_repo(request)
-        await thread_meta_repo.delete(thread_id)
+        thread_store = get_thread_store(request)
+        await thread_store.delete(thread_id)
     except Exception:
         logger.debug("Could not delete thread_meta for %s (not critical)", sanitize_log_param(thread_id))
 
@@ -227,17 +228,17 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
     and an empty checkpoint (so state endpoints work immediately).
     Idempotent: returns the existing record when ``thread_id`` already exists.
     """
-    from app.gateway.deps import get_thread_meta_repo
+    from app.gateway.deps import get_thread_store
 
     checkpointer = get_checkpointer(request)
-    thread_meta_repo = get_thread_meta_repo(request)
+    thread_store = get_thread_store(request)
     thread_id = body.thread_id or str(uuid.uuid4())
     now = time.time()
     # ``body.metadata`` is already stripped of server-reserved keys by
     # ``ThreadCreateRequest._strip_reserved`` — see the model definition.
 
     # Idempotency: return existing record when already present
-    existing_record = await thread_meta_repo.get(thread_id)
+    existing_record = await thread_store.get(thread_id)
     if existing_record is not None:
         return ThreadResponse(
             thread_id=thread_id,
@@ -249,7 +250,7 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
 
     # Write thread_meta so the thread appears in /threads/search immediately
     try:
-        await thread_meta_repo.create(
+        await thread_store.create(
             thread_id,
             assistant_id=getattr(body, "assistant_id", None),
             metadata=body.metadata,
@@ -293,9 +294,9 @@ async def search_threads(body: ThreadSearchRequest, request: Request) -> list[Th
     Delegates to the configured ThreadMetaStore implementation
     (SQL-backed for sqlite/postgres, Store-backed for memory mode).
     """
-    from app.gateway.deps import get_thread_meta_repo
+    from app.gateway.deps import get_thread_store
 
-    repo = get_thread_meta_repo(request)
+    repo = get_thread_store(request)
     rows = await repo.search(
         metadata=body.metadata or None,
         status=body.status,
@@ -320,22 +321,22 @@ async def search_threads(body: ThreadSearchRequest, request: Request) -> list[Th
 @require_permission("threads", "write", owner_check=True, require_existing=True)
 async def patch_thread(thread_id: str, body: ThreadPatchRequest, request: Request) -> ThreadResponse:
     """Merge metadata into a thread record."""
-    from app.gateway.deps import get_thread_meta_repo
+    from app.gateway.deps import get_thread_store
 
-    thread_meta_repo = get_thread_meta_repo(request)
-    record = await thread_meta_repo.get(thread_id)
+    thread_store = get_thread_store(request)
+    record = await thread_store.get(thread_id)
     if record is None:
         raise HTTPException(status_code=404, detail=f"Thread {thread_id} not found")
 
     # ``body.metadata`` already stripped by ``ThreadPatchRequest._strip_reserved``.
     try:
-        await thread_meta_repo.update_metadata(thread_id, body.metadata)
+        await thread_store.update_metadata(thread_id, body.metadata)
     except Exception:
         logger.exception("Failed to patch thread %s", sanitize_log_param(thread_id))
         raise HTTPException(status_code=500, detail="Failed to update thread")
 
     # Re-read to get the merged metadata + refreshed updated_at
-    record = await thread_meta_repo.get(thread_id) or record
+    record = await thread_store.get(thread_id) or record
     return ThreadResponse(
         thread_id=thread_id,
         status=record.get("status", "idle"),
@@ -354,12 +355,12 @@ async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
     execution status from the checkpointer.  Falls back to the checkpointer
     alone for threads that pre-date ThreadMetaStore adoption (backward compat).
     """
-    from app.gateway.deps import get_thread_meta_repo
+    from app.gateway.deps import get_thread_store
 
-    thread_meta_repo = get_thread_meta_repo(request)
+    thread_store = get_thread_store(request)
     checkpointer = get_checkpointer(request)
 
-    record: dict | None = await thread_meta_repo.get(thread_id)
+    record: dict | None = await thread_store.get(thread_id)
 
     # Derive accurate status from the checkpointer
     config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
@@ -402,6 +403,165 @@ async def get_thread(thread_id: str, request: Request) -> ThreadResponse:
     )
 
 
+# ---------------------------------------------------------------------------
+# Event-store-backed message loader
+# ---------------------------------------------------------------------------
+
+_LEGACY_CMD_INNER_CONTENT_RE = re.compile(
+    r"ToolMessage\(content=(?P<q>['\"])(?P<inner>.*?)(?P=q)",
+    re.DOTALL,
+)
+
+
+def _sanitize_legacy_command_repr(content_field: Any) -> Any:
+    """Recover the inner ToolMessage text from a legacy ``str(Command(...))`` repr.
+
+    Runs captured before the ``on_tool_end`` fix in ``journal.py`` stored
+    ``str(Command(update={'messages':[ToolMessage(content='X', ...)]}))`` as the
+    tool_result content. New runs store ``'X'`` directly. For legacy rows, try
+    to extract ``'X'`` defensively; return the original string if extraction
+    fails (still no worse than the checkpoint fallback for summarized threads).
+    """
+    if not isinstance(content_field, str) or not content_field.startswith("Command(update="):
+        return content_field
+    match = _LEGACY_CMD_INNER_CONTENT_RE.search(content_field)
+    return match.group("inner") if match else content_field
+
+
+async def _get_event_store_messages(request: Request, thread_id: str) -> list[dict] | None:
+    """Load the full message stream for ``thread_id`` from the event store.
+
+    The event store is append-only and unaffected by summarization — the
+    checkpoint's ``channel_values["messages"]`` is rewritten in-place when the
+    SummarizationMiddleware runs, which drops all pre-summarize messages. The
+    event store retains the full transcript, so callers in Gateway mode should
+    prefer it for rendering the conversation history.
+
+    In addition to the core message content, this helper attaches two extra
+    fields to every returned dict:
+
+    - ``run_id``: the ``run_id`` of the event that produced this message.
+      Always present.
+    - ``feedback``: thumbs-up/down data. Present only on the **final
+      ``ai_message`` of each run** (matching the per-run feedback semantics
+      of ``POST /api/threads/{id}/runs/{run_id}/feedback``). The frontend uses
+      the presence of this field to decide whether to render the feedback
+      button, which sidesteps the positional-index mapping bug that an
+      out-of-band ``/messages`` fetch exhibited.
+
+    Behaviour contract:
+
+    - **Full pagination.** ``RunEventStore.list_messages`` returns the newest
+      ``limit`` records when no cursor is given, so a fixed limit silently
+      drops older messages on long threads. We size the read from
+      ``count_messages()`` and then page forward with ``after_seq`` cursors.
+    - **Copy-on-read.** Each content dict is copied before ``id`` is patched
+      so the live store object is never mutated; ``MemoryRunEventStore``
+      returns live references.
+    - **Stable ids.** Messages with ``id=None`` (human + tool_result) receive
+      a deterministic ``uuid5(NAMESPACE_URL, f"{thread_id}:{seq}")`` so React
+      keys are stable across requests without altering stored data. AI messages
+      retain their LLM-assigned ``lc_run--*`` ids.
+    - **Legacy Command repr.** Rows captured before the ``journal.py``
+      ``on_tool_end`` fix stored ``str(Command(update={...}))`` as the tool
+      result content. ``_sanitize_legacy_command_repr`` extracts the inner
+      ToolMessage text.
+    - **User context.** ``DbRunEventStore`` is user-scoped by default via
+      ``resolve_user_id(AUTO)`` in ``runtime/user_context.py``. This helper
+      must run inside a request where ``@require_permission`` has populated
+      the user contextvar. Both callers below are decorated appropriately.
+      Do not call this helper from CLI or migration scripts without passing
+      ``user_id=None`` explicitly to the underlying store methods.
+
+    Returns ``None`` when the event store is not configured or has no message
+    events for this thread, so callers fall back to checkpoint messages.
+    """
+    try:
+        event_store = get_run_event_store(request)
+    except Exception:
+        return None
+
+    try:
+        total = await event_store.count_messages(thread_id)
+    except Exception:
+        logger.exception("count_messages failed for thread %s", sanitize_log_param(thread_id))
+        return None
+    if not total:
+        return None
+
+    # Batch by page_size to keep memory bounded for very long threads.
+    page_size = 500
+    collected: list[dict] = []
+    after_seq: int | None = None
+    while True:
+        try:
+            page = await event_store.list_messages(thread_id, limit=page_size, after_seq=after_seq)
+        except Exception:
+            logger.exception("list_messages failed for thread %s", sanitize_log_param(thread_id))
+            return None
+        if not page:
+            break
+        collected.extend(page)
+        if len(page) < page_size:
+            break
+        next_cursor = page[-1].get("seq")
+        if next_cursor is None or (after_seq is not None and next_cursor <= after_seq):
+            break
+        after_seq = next_cursor
+
+    # Build the message list; track the final ``ai_message`` index per run so
+    # feedback can be attached at the right position (matches thread_runs.py).
+    messages: list[dict] = []
+    last_ai_per_run: dict[str, int] = {}
+    for evt in collected:
+        raw = evt.get("content")
+        if not isinstance(raw, dict) or "type" not in raw:
+            continue
+        content = dict(raw)
+        if content.get("id") is None:
+            content["id"] = str(uuid.uuid5(uuid.NAMESPACE_URL, f"{thread_id}:{evt['seq']}"))
+        if content.get("type") == "tool":
+            content["content"] = _sanitize_legacy_command_repr(content.get("content"))
+        run_id = evt.get("run_id")
+        if run_id:
+            content["run_id"] = run_id
+        if evt.get("event_type") == "ai_message" and run_id:
+            last_ai_per_run[run_id] = len(messages)
+        messages.append(content)
+
+    if not messages:
+        return None
+
+    # Attach feedback to the final ai_message of each run. If the feedback
+    # subsystem is unavailable, leave the ``feedback`` field absent entirely
+    # so the frontend hides the button rather than showing it over a broken
+    # write path.
+    feedback_available = False
+    feedback_map: dict[str, dict] = {}
+    try:
+        feedback_repo = get_feedback_repo(request)
+        user_id = await get_current_user(request)
+        feedback_map = await feedback_repo.list_by_thread_grouped(thread_id, user_id=user_id)
+        feedback_available = True
+    except Exception:
+        logger.exception("feedback lookup failed for thread %s", sanitize_log_param(thread_id))
+
+    if feedback_available:
+        for run_id, idx in last_ai_per_run.items():
+            fb = feedback_map.get(run_id)
+            messages[idx]["feedback"] = (
+                {
+                    "feedback_id": fb["feedback_id"],
+                    "rating": fb["rating"],
+                    "comment": fb.get("comment"),
+                }
+                if fb
+                else None
+            )
+
+    return messages
+
+
 @router.get("/{thread_id}/state", response_model=ThreadStateResponse)
 @require_permission("threads", "read", owner_check=True)
 async def get_thread_state(thread_id: str, request: Request) -> ThreadStateResponse:
@@ -440,8 +600,15 @@ async def get_thread_state(thread_id: str, request: Request) -> ThreadStateRespo
     next_tasks = [t.name for t in tasks_raw if hasattr(t, "name")]
     tasks = [{"id": getattr(t, "id", ""), "name": getattr(t, "name", "")} for t in tasks_raw]
 
+    values = serialize_channel_values(channel_values)
+
+    # Prefer event-store messages: append-only, immune to summarization.
+    es_messages = await _get_event_store_messages(request, thread_id)
+    if es_messages is not None:
+        values["messages"] = es_messages
+
     return ThreadStateResponse(
-        values=serialize_channel_values(channel_values),
+        values=values,
         next=next_tasks,
         metadata=metadata,
         checkpoint={"id": checkpoint_id, "ts": str(metadata.get("created_at", ""))},
@@ -462,10 +629,10 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
     ThreadMetaStore abstraction so that ``/threads/search`` reflects the
     change immediately in both sqlite and memory backends.
     """
-    from app.gateway.deps import get_thread_meta_repo
+    from app.gateway.deps import get_thread_store
 
     checkpointer = get_checkpointer(request)
-    thread_meta_repo = get_thread_meta_repo(request)
+    thread_store = get_thread_store(request)
 
     # checkpoint_ns must be present in the config for aput — default to ""
     # (the root graph namespace).  checkpoint_id is optional; omitting it
@@ -529,7 +696,7 @@ async def update_thread_state(thread_id: str, body: ThreadStateUpdateRequest, re
         new_title = body.values["title"]
         if new_title:  # Skip empty strings and None
             try:
-                await thread_meta_repo.update_display_name(thread_id, new_title)
+                await thread_store.update_display_name(thread_id, new_title)
             except Exception:
                 logger.debug("Failed to sync title to thread_meta for %s (non-fatal)", sanitize_log_param(thread_id))
 
@@ -559,6 +726,11 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request
     if body.before:
         config["configurable"]["checkpoint_id"] = body.before
 
+    # Load the full event-store message stream once; attach to the latest
+    # checkpoint entry only (matching the prior semantics). The event store
+    # is append-only and immune to summarization.
+    es_messages = await _get_event_store_messages(request, thread_id)
+
     entries: list[HistoryEntry] = []
     is_latest_checkpoint = True
     try:
@@ -582,11 +754,17 @@ async def get_thread_history(thread_id: str, body: ThreadHistoryRequest, request
             if thread_data := channel_values.get("thread_data"):
                 values["thread_data"] = thread_data
 
-            # Attach messages from checkpointer only for the latest checkpoint
+            # Attach messages only to the latest checkpoint. Prefer the
+            # event-store stream (complete and unaffected by summarization);
+            # fall back to checkpoint channel_values when the event store is
+            # unavailable or empty.
             if is_latest_checkpoint:
-                messages = channel_values.get("messages")
-                if messages:
-                    values["messages"] = serialize_channel_values({"messages": messages}).get("messages", [])
+                if es_messages is not None:
+                    values["messages"] = es_messages
+                else:
+                    messages = channel_values.get("messages")
+                    if messages:
+                        values["messages"] = serialize_channel_values({"messages": messages}).get("messages", [])
             is_latest_checkpoint = False
 
             # Derive next tasks

backend/app/gateway/services.py

@@ -229,15 +229,15 @@ async def start_run(
     # even for threads that were never explicitly created via POST /threads
     # (e.g. stateless runs).
     try:
-        existing = await run_ctx.thread_meta_repo.get(thread_id)
+        existing = await run_ctx.thread_store.get(thread_id)
         if existing is None:
-            await run_ctx.thread_meta_repo.create(
+            await run_ctx.thread_store.create(
                 thread_id,
                 assistant_id=body.assistant_id,
                 metadata=body.metadata,
             )
         else:
-            await run_ctx.thread_meta_repo.update_status(thread_id, "running")
+            await run_ctx.thread_store.update_status(thread_id, "running")
     except Exception:
         logger.warning("Failed to upsert thread_meta for %s (non-fatal)", sanitize_log_param(thread_id))
 
@@ -285,7 +285,7 @@ async def start_run(
     record.task = task
 
     # Title sync is handled by worker.py's finally block which reads the
-    # title from the checkpoint and calls thread_meta_repo.update_display_name
+    # title from the checkpoint and calls thread_store.update_display_name
     # after the run completes.
 
     return record

backend/docs/TITLE_GENERATION_IMPLEMENTATION.md

@@ -124,7 +124,7 @@ title:
 # checkpointer.py
 from langgraph.checkpoint.sqlite import SqliteSaver
 
-checkpointer = SqliteSaver.from_conn_string("checkpoints.db")
+checkpointer = SqliteSaver.from_conn_string("deerflow.db")
 ```
 
 ```json

backend/packages/harness/deerflow/agents/__init__.py

@@ -1,4 +1,3 @@
-from .checkpointer import get_checkpointer, make_checkpointer, reset_checkpointer
 from .factory import create_deerflow_agent
 from .features import Next, Prev, RuntimeFeatures
 from .lead_agent import make_lead_agent
@@ -18,7 +17,4 @@ __all__ = [
     "make_lead_agent",
     "SandboxState",
     "ThreadState",
-    "get_checkpointer",
-    "reset_checkpointer",
-    "make_checkpointer",
 ]

backend/packages/harness/deerflow/client.py

@@ -240,7 +240,7 @@ class DeerFlowClient:
         }
         checkpointer = self._checkpointer
         if checkpointer is None:
-            from deerflow.agents.checkpointer import get_checkpointer
+            from deerflow.runtime.checkpointer import get_checkpointer
 
             checkpointer = get_checkpointer()
         if checkpointer is not None:
@@ -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/config/database_config.py

@@ -4,8 +4,12 @@ Controls BOTH the LangGraph checkpointer and the DeerFlow application
 persistence layer (runs, threads metadata, users, etc.). The user
 configures one backend; the system handles physical separation details.
 
-SQLite mode: checkpointer and app use different .db files in the same
-directory to avoid write-lock contention. This is automatic.
+SQLite mode: checkpointer and app share a single .db file
+({sqlite_dir}/deerflow.db) with WAL journal mode enabled on every
+connection. WAL allows concurrent readers and a single writer without
+blocking, making a unified file safe for both workloads.  Writers
+that contend for the lock wait via the default 5-second sqlite3
+busy timeout rather than failing immediately.
 
 Postgres mode: both use the same database URL but maintain independent
 connection pools with different lifecycles.
@@ -40,7 +44,7 @@ class DatabaseConfig(BaseModel):
     )
     sqlite_dir: str = Field(
         default=".deer-flow/data",
-        description=("Directory for SQLite database files. Checkpointer uses {sqlite_dir}/checkpoints.db, application data uses {sqlite_dir}/app.db."),
+        description=("Directory for the SQLite database file. Both checkpointer and application data share {sqlite_dir}/deerflow.db."),
     )
     postgres_url: str = Field(
         default="",
@@ -69,21 +73,27 @@ class DatabaseConfig(BaseModel):
 
         return str(Path(self.sqlite_dir).resolve())
 
+    @property
+    def sqlite_path(self) -> str:
+        """Unified SQLite file path shared by checkpointer and app."""
+        return os.path.join(self._resolved_sqlite_dir, "deerflow.db")
+
+    # Backward-compatible aliases
     @property
     def checkpointer_sqlite_path(self) -> str:
-        """SQLite file path for the LangGraph checkpointer."""
-        return os.path.join(self._resolved_sqlite_dir, "checkpoints.db")
+        """SQLite file path for the LangGraph checkpointer (alias for sqlite_path)."""
+        return self.sqlite_path
 
     @property
     def app_sqlite_path(self) -> str:
-        """SQLite file path for application ORM data."""
-        return os.path.join(self._resolved_sqlite_dir, "app.db")
+        """SQLite file path for application ORM data (alias for sqlite_path)."""
+        return self.sqlite_path
 
     @property
     def app_sqlalchemy_url(self) -> str:
         """SQLAlchemy async URL for the application ORM engine."""
         if self.backend == "sqlite":
-            return f"sqlite+aiosqlite:///{self.app_sqlite_path}"
+            return f"sqlite+aiosqlite:///{self.sqlite_path}"
         if self.backend == "postgres":
             url = self.postgres_url
             if url.startswith("postgresql://"):

backend/packages/harness/deerflow/persistence/engine.py

@@ -98,6 +98,11 @@ async def init_engine(
         # SQLite deployment (TC-UPG-06 in AUTH_TEST_PLAN.md). The companion
         # ``synchronous=NORMAL`` is the safe-and-fast pairing — fsync only
         # at WAL checkpoint boundaries instead of every commit.
+        # Note: we do not set PRAGMA busy_timeout here — Python's sqlite3
+        # driver already defaults to a 5-second busy timeout (see the
+        # ``timeout`` kwarg of ``sqlite3.connect``), and aiosqlite /
+        # SQLAlchemy's aiosqlite dialect inherit that default.  Setting
+        # it again would be a no-op.
         @event.listens_for(_engine.sync_engine, "connect")
         def _enable_sqlite_wal(dbapi_conn, _record):  # noqa: ARG001 — SQLAlchemy contract
             cursor = dbapi_conn.cursor()

backend/packages/harness/deerflow/persistence/feedback/model.py

@@ -4,7 +4,7 @@ from __future__ import annotations
 
 from datetime import UTC, datetime
 
-from sqlalchemy import DateTime, String, Text
+from sqlalchemy import DateTime, String, Text, UniqueConstraint
 from sqlalchemy.orm import Mapped, mapped_column
 
 from deerflow.persistence.base import Base
@@ -13,10 +13,14 @@ from deerflow.persistence.base import Base
 class FeedbackRow(Base):
     __tablename__ = "feedback"
 
+    __table_args__ = (
+        UniqueConstraint("thread_id", "run_id", "user_id", name="uq_feedback_thread_run_user"),
+    )
+
     feedback_id: Mapped[str] = mapped_column(String(64), primary_key=True)
     run_id: Mapped[str] = mapped_column(String(64), nullable=False, index=True)
     thread_id: Mapped[str] = mapped_column(String(64), nullable=False, index=True)
-    owner_id: Mapped[str | None] = mapped_column(String(64), index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), index=True)
     message_id: Mapped[str | None] = mapped_column(String(64))
     # message_id is an optional RunEventStore event identifier —
     # allows feedback to target a specific message or the entire run

backend/packages/harness/deerflow/persistence/feedback/sql.py

@@ -12,7 +12,7 @@ from sqlalchemy import case, func, select
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from deerflow.persistence.feedback.model import FeedbackRow
-from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_owner_id
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
 
 
 class FeedbackRepository:
@@ -33,19 +33,19 @@ class FeedbackRepository:
         run_id: str,
         thread_id: str,
         rating: int,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
         message_id: str | None = None,
         comment: str | None = None,
     ) -> dict:
         """Create a feedback record. rating must be +1 or -1."""
         if rating not in (1, -1):
             raise ValueError(f"rating must be +1 or -1, got {rating}")
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="FeedbackRepository.create")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.create")
         row = FeedbackRow(
             feedback_id=str(uuid.uuid4()),
             run_id=run_id,
             thread_id=thread_id,
-            owner_id=resolved_owner_id,
+            user_id=resolved_user_id,
             message_id=message_id,
             rating=rating,
             comment=comment,
@@ -61,14 +61,14 @@ class FeedbackRepository:
         self,
         feedback_id: str,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> dict | None:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="FeedbackRepository.get")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.get")
         async with self._sf() as session:
             row = await session.get(FeedbackRow, feedback_id)
             if row is None:
                 return None
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return None
             return self._row_to_dict(row)
 
@@ -78,12 +78,12 @@ class FeedbackRepository:
         run_id: str,
         *,
         limit: int = 100,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> list[dict]:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="FeedbackRepository.list_by_run")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.list_by_run")
         stmt = select(FeedbackRow).where(FeedbackRow.thread_id == thread_id, FeedbackRow.run_id == run_id)
-        if resolved_owner_id is not None:
-            stmt = stmt.where(FeedbackRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(FeedbackRow.user_id == resolved_user_id)
         stmt = stmt.order_by(FeedbackRow.created_at.asc()).limit(limit)
         async with self._sf() as session:
             result = await session.execute(stmt)
@@ -94,12 +94,12 @@ class FeedbackRepository:
         thread_id: str,
         *,
         limit: int = 100,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> list[dict]:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="FeedbackRepository.list_by_thread")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.list_by_thread")
         stmt = select(FeedbackRow).where(FeedbackRow.thread_id == thread_id)
-        if resolved_owner_id is not None:
-            stmt = stmt.where(FeedbackRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(FeedbackRow.user_id == resolved_user_id)
         stmt = stmt.order_by(FeedbackRow.created_at.asc()).limit(limit)
         async with self._sf() as session:
             result = await session.execute(stmt)
@@ -109,19 +109,97 @@ class FeedbackRepository:
         self,
         feedback_id: str,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> bool:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="FeedbackRepository.delete")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.delete")
         async with self._sf() as session:
             row = await session.get(FeedbackRow, feedback_id)
             if row is None:
                 return False
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return False
             await session.delete(row)
             await session.commit()
             return True
 
+    async def upsert(
+        self,
+        *,
+        run_id: str,
+        thread_id: str,
+        rating: int,
+        user_id: str | None | _AutoSentinel = AUTO,
+        comment: str | None = None,
+    ) -> dict:
+        """Create or update feedback for (thread_id, run_id, user_id). rating must be +1 or -1."""
+        if rating not in (1, -1):
+            raise ValueError(f"rating must be +1 or -1, got {rating}")
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.upsert")
+        async with self._sf() as session:
+            stmt = select(FeedbackRow).where(
+                FeedbackRow.thread_id == thread_id,
+                FeedbackRow.run_id == run_id,
+                FeedbackRow.user_id == resolved_user_id,
+            )
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            if row is not None:
+                row.rating = rating
+                row.comment = comment
+                row.created_at = datetime.now(UTC)
+            else:
+                row = FeedbackRow(
+                    feedback_id=str(uuid.uuid4()),
+                    run_id=run_id,
+                    thread_id=thread_id,
+                    user_id=resolved_user_id,
+                    rating=rating,
+                    comment=comment,
+                    created_at=datetime.now(UTC),
+                )
+                session.add(row)
+            await session.commit()
+            await session.refresh(row)
+            return self._row_to_dict(row)
+
+    async def delete_by_run(
+        self,
+        *,
+        thread_id: str,
+        run_id: str,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> bool:
+        """Delete the current user's feedback for a run. Returns True if a record was deleted."""
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.delete_by_run")
+        async with self._sf() as session:
+            stmt = select(FeedbackRow).where(
+                FeedbackRow.thread_id == thread_id,
+                FeedbackRow.run_id == run_id,
+                FeedbackRow.user_id == resolved_user_id,
+            )
+            result = await session.execute(stmt)
+            row = result.scalar_one_or_none()
+            if row is None:
+                return False
+            await session.delete(row)
+            await session.commit()
+            return True
+
+    async def list_by_thread_grouped(
+        self,
+        thread_id: str,
+        *,
+        user_id: str | None | _AutoSentinel = AUTO,
+    ) -> dict[str, dict]:
+        """Return feedback grouped by run_id for a thread: {run_id: feedback_dict}."""
+        resolved_user_id = resolve_user_id(user_id, method_name="FeedbackRepository.list_by_thread_grouped")
+        stmt = select(FeedbackRow).where(FeedbackRow.thread_id == thread_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(FeedbackRow.user_id == resolved_user_id)
+        async with self._sf() as session:
+            result = await session.execute(stmt)
+            return {row.run_id: self._row_to_dict(row) for row in result.scalars()}
+
     async def aggregate_by_run(self, thread_id: str, run_id: str) -> dict:
         """Aggregate feedback stats for a run using database-side counting."""
         stmt = select(

backend/packages/harness/deerflow/persistence/migrations/alembic.ini

@@ -2,7 +2,7 @@
 script_location = %(here)s
 # Default URL for offline mode / autogenerate.
 # Runtime uses engine from DeerFlow config.
-sqlalchemy.url = sqlite+aiosqlite:///./data/app.db
+sqlalchemy.url = sqlite+aiosqlite:///./data/deerflow.db
 
 [loggers]
 keys = root,sqlalchemy,alembic

backend/packages/harness/deerflow/persistence/models/run_event.py

@@ -19,7 +19,7 @@ class RunEventRow(Base):
     # Owner of the conversation this event belongs to. Nullable for data
     # created before auth was introduced; populated by auth middleware on
     # new writes and by the boot-time orphan migration on existing rows.
-    owner_id: Mapped[str | None] = mapped_column(String(64), nullable=True, index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), nullable=True, index=True)
     event_type: Mapped[str] = mapped_column(String(32), nullable=False)
     category: Mapped[str] = mapped_column(String(16), nullable=False)
     # "message" | "trace" | "lifecycle"

backend/packages/harness/deerflow/persistence/run/model.py

@@ -16,7 +16,7 @@ class RunRow(Base):
     run_id: Mapped[str] = mapped_column(String(64), primary_key=True)
     thread_id: Mapped[str] = mapped_column(String(64), nullable=False, index=True)
     assistant_id: Mapped[str | None] = mapped_column(String(128))
-    owner_id: Mapped[str | None] = mapped_column(String(64), index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), index=True)
     status: Mapped[str] = mapped_column(String(20), default="pending")
     # "pending" | "running" | "success" | "error" | "timeout" | "interrupted"
 

backend/packages/harness/deerflow/persistence/run/sql.py

@@ -16,7 +16,7 @@ from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from deerflow.persistence.run.model import RunRow
 from deerflow.runtime.runs.store.base import RunStore
-from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_owner_id
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
 
 
 class RunRepository(RunStore):
@@ -69,7 +69,7 @@ class RunRepository(RunStore):
         *,
         thread_id,
         assistant_id=None,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
         status="pending",
         multitask_strategy="reject",
         metadata=None,
@@ -78,13 +78,13 @@ class RunRepository(RunStore):
         created_at=None,
         follow_up_to_run_id=None,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="RunRepository.put")
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.put")
         now = datetime.now(UTC)
         row = RunRow(
             run_id=run_id,
             thread_id=thread_id,
             assistant_id=assistant_id,
-            owner_id=resolved_owner_id,
+            user_id=resolved_user_id,
             status=status,
             multitask_strategy=multitask_strategy,
             metadata_json=self._safe_json(metadata) or {},
@@ -102,14 +102,14 @@ class RunRepository(RunStore):
         self,
         run_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="RunRepository.get")
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.get")
         async with self._sf() as session:
             row = await session.get(RunRow, run_id)
             if row is None:
                 return None
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return None
             return self._row_to_dict(row)
 
@@ -117,13 +117,13 @@ class RunRepository(RunStore):
         self,
         thread_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
         limit=100,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="RunRepository.list_by_thread")
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.list_by_thread")
         stmt = select(RunRow).where(RunRow.thread_id == thread_id)
-        if resolved_owner_id is not None:
-            stmt = stmt.where(RunRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunRow.user_id == resolved_user_id)
         stmt = stmt.order_by(RunRow.created_at.desc()).limit(limit)
         async with self._sf() as session:
             result = await session.execute(stmt)
@@ -141,14 +141,14 @@ class RunRepository(RunStore):
         self,
         run_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="RunRepository.delete")
+        resolved_user_id = resolve_user_id(user_id, method_name="RunRepository.delete")
         async with self._sf() as session:
             row = await session.get(RunRow, run_id)
             if row is None:
                 return
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return
             await session.delete(row)
             await session.commit()

backend/packages/harness/deerflow/persistence/thread_meta/__init__.py

@@ -1,13 +1,38 @@
 """Thread metadata persistence — ORM, abstract store, and concrete implementations."""
 
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
 from deerflow.persistence.thread_meta.base import ThreadMetaStore
 from deerflow.persistence.thread_meta.memory import MemoryThreadMetaStore
 from deerflow.persistence.thread_meta.model import ThreadMetaRow
 from deerflow.persistence.thread_meta.sql import ThreadMetaRepository
 
+if TYPE_CHECKING:
+    from langgraph.store.base import BaseStore
+    from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
 __all__ = [
     "MemoryThreadMetaStore",
     "ThreadMetaRepository",
     "ThreadMetaRow",
     "ThreadMetaStore",
+    "make_thread_store",
 ]
+
+
+def make_thread_store(
+    session_factory: async_sessionmaker[AsyncSession] | None,
+    store: BaseStore | None = None,
+) -> ThreadMetaStore:
+    """Create the appropriate ThreadMetaStore based on available backends.
+
+    Returns a SQL-backed repository when a session factory is available,
+    otherwise falls back to the in-memory LangGraph Store implementation.
+    """
+    if session_factory is not None:
+        return ThreadMetaRepository(session_factory)
+    if store is None:
+        raise ValueError("make_thread_store requires either a session_factory (SQL) or a store (memory)")
+    return MemoryThreadMetaStore(store)

backend/packages/harness/deerflow/persistence/thread_meta/base.py

@@ -3,12 +3,21 @@
 Implementations:
 - ThreadMetaRepository: SQL-backed (sqlite / postgres via SQLAlchemy)
 - MemoryThreadMetaStore: wraps LangGraph BaseStore (memory mode)
+
+All mutating and querying methods accept a ``user_id`` parameter with
+three-state semantics (see :mod:`deerflow.runtime.user_context`):
+
+- ``AUTO`` (default): resolve from the request-scoped contextvar.
+- Explicit ``str``: use the provided value verbatim.
+- Explicit ``None``: bypass owner filtering (migration/CLI only).
 """
 
 from __future__ import annotations
 
 import abc
 
+from deerflow.runtime.user_context import AUTO, _AutoSentinel
+
 
 class ThreadMetaStore(abc.ABC):
     @abc.abstractmethod
@@ -17,14 +26,14 @@ class ThreadMetaStore(abc.ABC):
         thread_id: str,
         *,
         assistant_id: str | None = None,
-        owner_id: str | None = None,
+        user_id: str | None | _AutoSentinel = AUTO,
         display_name: str | None = None,
         metadata: dict | None = None,
     ) -> dict:
         pass
 
     @abc.abstractmethod
-    async def get(self, thread_id: str) -> dict | None:
+    async def get(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> dict | None:
         pass
 
     @abc.abstractmethod
@@ -35,26 +44,33 @@ class ThreadMetaStore(abc.ABC):
         status: str | None = None,
         limit: int = 100,
         offset: int = 0,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> list[dict]:
         pass
 
     @abc.abstractmethod
-    async def update_display_name(self, thread_id: str, display_name: str) -> None:
+    async def update_display_name(self, thread_id: str, display_name: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
         pass
 
     @abc.abstractmethod
-    async def update_status(self, thread_id: str, status: str) -> None:
+    async def update_status(self, thread_id: str, status: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
         pass
 
     @abc.abstractmethod
-    async def update_metadata(self, thread_id: str, metadata: dict) -> None:
+    async def update_metadata(self, thread_id: str, metadata: dict, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
         """Merge ``metadata`` into the thread's metadata field.
 
         Existing keys are overwritten by the new values; keys absent from
-        ``metadata`` are preserved. No-op if the thread does not exist.
+        ``metadata`` are preserved. No-op if the thread does not exist
+        or the owner check fails.
         """
         pass
 
     @abc.abstractmethod
-    async def delete(self, thread_id: str) -> None:
+    async def check_access(self, thread_id: str, user_id: str, *, require_existing: bool = False) -> bool:
+        """Check if ``user_id`` has access to ``thread_id``."""
+        pass
+
+    @abc.abstractmethod
+    async def delete(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
         pass

backend/packages/harness/deerflow/persistence/thread_meta/memory.py

@@ -13,6 +13,7 @@ from typing import Any
 from langgraph.store.base import BaseStore
 
 from deerflow.persistence.thread_meta.base import ThreadMetaStore
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
 
 THREADS_NS: tuple[str, ...] = ("threads",)
 
@@ -21,20 +22,37 @@ class MemoryThreadMetaStore(ThreadMetaStore):
     def __init__(self, store: BaseStore) -> None:
         self._store = store
 
+    async def _get_owned_record(
+        self,
+        thread_id: str,
+        user_id: str | None | _AutoSentinel,
+        method_name: str,
+    ) -> dict | None:
+        """Fetch a record and verify ownership. Returns a mutable copy, or None."""
+        resolved = resolve_user_id(user_id, method_name=method_name)
+        item = await self._store.aget(THREADS_NS, thread_id)
+        if item is None:
+            return None
+        record = dict(item.value)
+        if resolved is not None and record.get("user_id") != resolved:
+            return None
+        return record
+
     async def create(
         self,
         thread_id: str,
         *,
         assistant_id: str | None = None,
-        owner_id: str | None = None,
+        user_id: str | None | _AutoSentinel = AUTO,
         display_name: str | None = None,
         metadata: dict | None = None,
     ) -> dict:
+        resolved_user_id = resolve_user_id(user_id, method_name="MemoryThreadMetaStore.create")
         now = time.time()
         record: dict[str, Any] = {
             "thread_id": thread_id,
             "assistant_id": assistant_id,
-            "owner_id": owner_id,
+            "user_id": resolved_user_id,
             "display_name": display_name,
             "status": "idle",
             "metadata": metadata or {},
@@ -45,9 +63,8 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         await self._store.aput(THREADS_NS, thread_id, record)
         return record
 
-    async def get(self, thread_id: str) -> dict | None:
-        item = await self._store.aget(THREADS_NS, thread_id)
-        return item.value if item is not None else None
+    async def get(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> dict | None:
+        return await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.get")
 
     async def search(
         self,
@@ -56,12 +73,16 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         status: str | None = None,
         limit: int = 100,
         offset: int = 0,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> list[dict]:
+        resolved_user_id = resolve_user_id(user_id, method_name="MemoryThreadMetaStore.search")
         filter_dict: dict[str, Any] = {}
         if metadata:
             filter_dict.update(metadata)
         if status:
             filter_dict["status"] = status
+        if resolved_user_id is not None:
+            filter_dict["user_id"] = resolved_user_id
 
         items = await self._store.asearch(
             THREADS_NS,
@@ -71,37 +92,45 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         )
         return [self._item_to_dict(item) for item in items]
 
-    async def update_display_name(self, thread_id: str, display_name: str) -> None:
+    async def check_access(self, thread_id: str, user_id: str, *, require_existing: bool = False) -> bool:
         item = await self._store.aget(THREADS_NS, thread_id)
         if item is None:
+            return not require_existing
+        record_user_id = item.value.get("user_id")
+        if record_user_id is None:
+            return True
+        return record_user_id == user_id
+
+    async def update_display_name(self, thread_id: str, display_name: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.update_display_name")
+        if record is None:
             return
-        record = dict(item.value)
         record["display_name"] = display_name
         record["updated_at"] = time.time()
         await self._store.aput(THREADS_NS, thread_id, record)
 
-    async def update_status(self, thread_id: str, status: str) -> None:
-        item = await self._store.aget(THREADS_NS, thread_id)
-        if item is None:
+    async def update_status(self, thread_id: str, status: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.update_status")
+        if record is None:
             return
-        record = dict(item.value)
         record["status"] = status
         record["updated_at"] = time.time()
         await self._store.aput(THREADS_NS, thread_id, record)
 
-    async def update_metadata(self, thread_id: str, metadata: dict) -> None:
-        """Merge ``metadata`` into the in-memory record. No-op if absent."""
-        item = await self._store.aget(THREADS_NS, thread_id)
-        if item is None:
+    async def update_metadata(self, thread_id: str, metadata: dict, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.update_metadata")
+        if record is None:
             return
-        record = dict(item.value)
         merged = dict(record.get("metadata") or {})
         merged.update(metadata)
         record["metadata"] = merged
         record["updated_at"] = time.time()
         await self._store.aput(THREADS_NS, thread_id, record)
 
-    async def delete(self, thread_id: str) -> None:
+    async def delete(self, thread_id: str, *, user_id: str | None | _AutoSentinel = AUTO) -> None:
+        record = await self._get_owned_record(thread_id, user_id, "MemoryThreadMetaStore.delete")
+        if record is None:
+            return
         await self._store.adelete(THREADS_NS, thread_id)
 
     @staticmethod
@@ -111,7 +140,7 @@ class MemoryThreadMetaStore(ThreadMetaStore):
         return {
             "thread_id": item.key,
             "assistant_id": val.get("assistant_id"),
-            "owner_id": val.get("owner_id"),
+            "user_id": val.get("user_id"),
             "display_name": val.get("display_name"),
             "status": val.get("status", "idle"),
             "metadata": val.get("metadata", {}),

backend/packages/harness/deerflow/persistence/thread_meta/model.py

@@ -15,7 +15,7 @@ class ThreadMetaRow(Base):
 
     thread_id: Mapped[str] = mapped_column(String(64), primary_key=True)
     assistant_id: Mapped[str | None] = mapped_column(String(128), index=True)
-    owner_id: Mapped[str | None] = mapped_column(String(64), index=True)
+    user_id: Mapped[str | None] = mapped_column(String(64), index=True)
     display_name: Mapped[str | None] = mapped_column(String(256))
     status: Mapped[str] = mapped_column(String(20), default="idle")
     metadata_json: Mapped[dict] = mapped_column(JSON, default=dict)

backend/packages/harness/deerflow/persistence/thread_meta/sql.py

@@ -10,7 +10,7 @@ from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from deerflow.persistence.thread_meta.base import ThreadMetaStore
 from deerflow.persistence.thread_meta.model import ThreadMetaRow
-from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_owner_id
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, resolve_user_id
 
 
 class ThreadMetaRepository(ThreadMetaStore):
@@ -32,18 +32,18 @@ class ThreadMetaRepository(ThreadMetaStore):
         thread_id: str,
         *,
         assistant_id: str | None = None,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
         display_name: str | None = None,
         metadata: dict | None = None,
     ) -> dict:
-        # Auto-resolve owner_id from contextvar when AUTO; explicit None
+        # Auto-resolve user_id from contextvar when AUTO; explicit None
         # creates an orphan row (used by migration scripts).
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.create")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.create")
         now = datetime.now(UTC)
         row = ThreadMetaRow(
             thread_id=thread_id,
             assistant_id=assistant_id,
-            owner_id=resolved_owner_id,
+            user_id=resolved_user_id,
             display_name=display_name,
             metadata_json=metadata or {},
             created_at=now,
@@ -59,40 +59,34 @@ class ThreadMetaRepository(ThreadMetaStore):
         self,
         thread_id: str,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> dict | None:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.get")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.get")
         async with self._sf() as session:
             row = await session.get(ThreadMetaRow, thread_id)
             if row is None:
                 return None
-            # Enforce owner filter unless explicitly bypassed (owner_id=None).
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            # Enforce owner filter unless explicitly bypassed (user_id=None).
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return None
             return self._row_to_dict(row)
 
-    async def list_by_owner(self, owner_id: str, *, limit: int = 100, offset: int = 0) -> list[dict]:
-        stmt = select(ThreadMetaRow).where(ThreadMetaRow.owner_id == owner_id).order_by(ThreadMetaRow.updated_at.desc()).limit(limit).offset(offset)
-        async with self._sf() as session:
-            result = await session.execute(stmt)
-            return [self._row_to_dict(r) for r in result.scalars()]
-
-    async def check_access(self, thread_id: str, owner_id: str, *, require_existing: bool = False) -> bool:
-        """Check if ``owner_id`` has access to ``thread_id``.
+    async def check_access(self, thread_id: str, user_id: str, *, require_existing: bool = False) -> bool:
+        """Check if ``user_id`` has access to ``thread_id``.
 
         Two modes — one row, two distinct semantics depending on what
         the caller is about to do:
 
         - ``require_existing=False`` (default, permissive):
           Returns True for: row missing (untracked legacy thread),
-          ``row.owner_id`` is None (shared / pre-auth data),
-          or ``row.owner_id == owner_id``. Use for **read-style**
+          ``row.user_id`` is None (shared / pre-auth data),
+          or ``row.user_id == user_id``. Use for **read-style**
           decorators where treating an untracked thread as accessible
           preserves backward-compat.
 
         - ``require_existing=True`` (strict):
           Returns True **only** when the row exists AND
-          (``row.owner_id == owner_id`` OR ``row.owner_id is None``).
+          (``row.user_id == user_id`` OR ``row.user_id is None``).
           Use for **destructive / mutating** decorators (DELETE, PATCH,
           state-update) so a thread that has *already been deleted*
           cannot be re-targeted by any caller — closing the
@@ -103,9 +97,9 @@ class ThreadMetaRepository(ThreadMetaStore):
             row = await session.get(ThreadMetaRow, thread_id)
             if row is None:
                 return not require_existing
-            if row.owner_id is None:
+            if row.user_id is None:
                 return True
-            return row.owner_id == owner_id
+            return row.user_id == user_id
 
     async def search(
         self,
@@ -114,17 +108,17 @@ class ThreadMetaRepository(ThreadMetaStore):
         status: str | None = None,
         limit: int = 100,
         offset: int = 0,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> list[dict]:
         """Search threads with optional metadata and status filters.
 
         Owner filter is enforced by default: caller must be in a user
-        context. Pass ``owner_id=None`` to bypass (migration/CLI).
+        context. Pass ``user_id=None`` to bypass (migration/CLI).
         """
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.search")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.search")
         stmt = select(ThreadMetaRow).order_by(ThreadMetaRow.updated_at.desc())
-        if resolved_owner_id is not None:
-            stmt = stmt.where(ThreadMetaRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(ThreadMetaRow.user_id == resolved_user_id)
         if status:
             stmt = stmt.where(ThreadMetaRow.status == status)
 
@@ -144,24 +138,24 @@ class ThreadMetaRepository(ThreadMetaStore):
                 result = await session.execute(stmt)
                 return [self._row_to_dict(r) for r in result.scalars()]
 
-    async def _check_ownership(self, session: AsyncSession, thread_id: str, resolved_owner_id: str | None) -> bool:
+    async def _check_ownership(self, session: AsyncSession, thread_id: str, resolved_user_id: str | None) -> bool:
         """Return True if the row exists and is owned (or filter bypassed)."""
-        if resolved_owner_id is None:
+        if resolved_user_id is None:
             return True  # explicit bypass
         row = await session.get(ThreadMetaRow, thread_id)
-        return row is not None and row.owner_id == resolved_owner_id
+        return row is not None and row.user_id == resolved_user_id
 
     async def update_display_name(
         self,
         thread_id: str,
         display_name: str,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> None:
         """Update the display_name (title) for a thread."""
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.update_display_name")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.update_display_name")
         async with self._sf() as session:
-            if not await self._check_ownership(session, thread_id, resolved_owner_id):
+            if not await self._check_ownership(session, thread_id, resolved_user_id):
                 return
             await session.execute(update(ThreadMetaRow).where(ThreadMetaRow.thread_id == thread_id).values(display_name=display_name, updated_at=datetime.now(UTC)))
             await session.commit()
@@ -171,11 +165,11 @@ class ThreadMetaRepository(ThreadMetaStore):
         thread_id: str,
         status: str,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> None:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.update_status")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.update_status")
         async with self._sf() as session:
-            if not await self._check_ownership(session, thread_id, resolved_owner_id):
+            if not await self._check_ownership(session, thread_id, resolved_user_id):
                 return
             await session.execute(update(ThreadMetaRow).where(ThreadMetaRow.thread_id == thread_id).values(status=status, updated_at=datetime.now(UTC)))
             await session.commit()
@@ -185,20 +179,20 @@ class ThreadMetaRepository(ThreadMetaStore):
         thread_id: str,
         metadata: dict,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> None:
         """Merge ``metadata`` into ``metadata_json``.
 
         Read-modify-write inside a single session/transaction so concurrent
         callers see consistent state. No-op if the row does not exist or
-        the owner_id check fails.
+        the user_id check fails.
         """
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.update_metadata")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.update_metadata")
         async with self._sf() as session:
             row = await session.get(ThreadMetaRow, thread_id)
             if row is None:
                 return
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return
             merged = dict(row.metadata_json or {})
             merged.update(metadata)
@@ -210,14 +204,14 @@ class ThreadMetaRepository(ThreadMetaStore):
         self,
         thread_id: str,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ) -> None:
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="ThreadMetaRepository.delete")
+        resolved_user_id = resolve_user_id(user_id, method_name="ThreadMetaRepository.delete")
         async with self._sf() as session:
             row = await session.get(ThreadMetaRow, thread_id)
             if row is None:
                 return
-            if resolved_owner_id is not None and row.owner_id != resolved_owner_id:
+            if resolved_user_id is not None and row.user_id != resolved_user_id:
                 return
             await session.delete(row)
             await session.commit()

backend/packages/harness/deerflow/runtime/__init__.py

@@ -5,12 +5,18 @@ Re-exports the public API of :mod:`~deerflow.runtime.runs` and
 directly from ``deerflow.runtime``.
 """
 
+from .checkpointer import checkpointer_context, get_checkpointer, make_checkpointer, reset_checkpointer
 from .runs import ConflictError, DisconnectMode, RunContext, RunManager, RunRecord, RunStatus, UnsupportedStrategyError, run_agent
 from .serialization import serialize, serialize_channel_values, serialize_lc_object, serialize_messages_tuple
 from .store import get_store, make_store, reset_store, store_context
 from .stream_bridge import END_SENTINEL, HEARTBEAT_SENTINEL, MemoryStreamBridge, StreamBridge, StreamEvent, make_stream_bridge
 
 __all__ = [
+    # checkpointer
+    "checkpointer_context",
+    "get_checkpointer",
+    "make_checkpointer",
+    "reset_checkpointer",
     # runs
     "ConflictError",
     "DisconnectMode",

backend/packages/harness/deerflow/runtime/checkpointer/async_provider.py

@@ -7,12 +7,12 @@ Supported backends: memory, sqlite, postgres.
 
 Usage (e.g. FastAPI lifespan)::
 
-    from deerflow.agents.checkpointer.async_provider import make_checkpointer
+    from deerflow.runtime.checkpointer.async_provider import make_checkpointer
 
     async with make_checkpointer() as checkpointer:
         app.state.checkpointer = checkpointer  # InMemorySaver if not configured
 
-For sync usage see :mod:`deerflow.agents.checkpointer.provider`.
+For sync usage see :mod:`deerflow.runtime.checkpointer.provider`.
 """
 
 from __future__ import annotations
@@ -24,12 +24,12 @@ from collections.abc import AsyncIterator
 
 from langgraph.types import Checkpointer
 
-from deerflow.agents.checkpointer.provider import (
+from deerflow.config.app_config import get_app_config
+from deerflow.runtime.checkpointer.provider import (
     POSTGRES_CONN_REQUIRED,
     POSTGRES_INSTALL,
     SQLITE_INSTALL,
 )
-from deerflow.config.app_config import get_app_config
 from deerflow.runtime.store._sqlite_utils import ensure_sqlite_parent_dir, resolve_sqlite_conn_str
 
 logger = logging.getLogger(__name__)

backend/packages/harness/deerflow/runtime/checkpointer/provider.py

@@ -7,7 +7,7 @@ Supported backends: memory, sqlite, postgres.
 
 Usage::
 
-    from deerflow.agents.checkpointer.provider import get_checkpointer, checkpointer_context
+    from deerflow.runtime.checkpointer.provider import get_checkpointer, checkpointer_context
 
     # Singleton — reused across calls, closed on process exit
     cp = get_checkpointer()

backend/packages/harness/deerflow/runtime/events/store/db.py

@@ -15,7 +15,7 @@ from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from deerflow.persistence.models.run_event import RunEventRow
 from deerflow.runtime.events.store.base import RunEventStore
-from deerflow.runtime.user_context import AUTO, _AutoSentinel, get_current_user, resolve_owner_id
+from deerflow.runtime.user_context import AUTO, _AutoSentinel, get_current_user, resolve_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -55,16 +55,22 @@ class DbRunEventStore(RunEventStore):
         return content, metadata or {}
 
     @staticmethod
-    def _owner_from_context() -> str | None:
-        """Soft read of owner_id from contextvar for write paths.
+    def _user_id_from_context() -> str | None:
+        """Soft read of user_id from contextvar for write paths.
 
         Returns ``None`` (no filter / no stamp) if contextvar is unset,
         which is the expected case for background worker writes. HTTP
         request writes will have the contextvar set by auth middleware
         and get their user_id stamped automatically.
+
+        Coerces ``user.id`` to ``str`` at the boundary: ``User.id`` is
+        typed as ``UUID`` by the auth layer, but ``run_events.user_id``
+        is ``VARCHAR(64)`` and aiosqlite cannot bind a raw UUID object
+        to a VARCHAR column ("type 'UUID' is not supported") — the
+        INSERT would silently roll back and the worker would hang.
         """
         user = get_current_user()
-        return user.id if user is not None else None
+        return str(user.id) if user is not None else None
 
     async def put(self, *, thread_id, run_id, event_type, category, content="", metadata=None, created_at=None):  # noqa: D401
         """Write a single event — low-frequency path only.
@@ -81,7 +87,7 @@ class DbRunEventStore(RunEventStore):
             metadata = {**(metadata or {}), "content_is_dict": True}
         else:
             db_content = content
-        owner_id = self._owner_from_context()
+        user_id = self._user_id_from_context()
         async with self._sf() as session:
             async with session.begin():
                 # Use FOR UPDATE to serialize seq assignment within a thread.
@@ -92,7 +98,7 @@ class DbRunEventStore(RunEventStore):
                 row = RunEventRow(
                     thread_id=thread_id,
                     run_id=run_id,
-                    owner_id=owner_id,
+                    user_id=user_id,
                     event_type=event_type,
                     category=category,
                     content=db_content,
@@ -106,7 +112,7 @@ class DbRunEventStore(RunEventStore):
     async def put_batch(self, events):
         if not events:
             return []
-        owner_id = self._owner_from_context()
+        user_id = self._user_id_from_context()
         async with self._sf() as session:
             async with session.begin():
                 # Get max seq for the thread (assume all events in batch belong to same thread).
@@ -130,7 +136,7 @@ class DbRunEventStore(RunEventStore):
                     row = RunEventRow(
                         thread_id=e["thread_id"],
                         run_id=e["run_id"],
-                        owner_id=e.get("owner_id", owner_id),
+                        user_id=e.get("user_id", user_id),
                         event_type=e["event_type"],
                         category=category,
                         content=db_content,
@@ -149,12 +155,12 @@ class DbRunEventStore(RunEventStore):
         limit=50,
         before_seq=None,
         after_seq=None,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="DbRunEventStore.list_messages")
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.list_messages")
         stmt = select(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.category == "message")
-        if resolved_owner_id is not None:
-            stmt = stmt.where(RunEventRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
         if before_seq is not None:
             stmt = stmt.where(RunEventRow.seq < before_seq)
         if after_seq is not None:
@@ -181,12 +187,12 @@ class DbRunEventStore(RunEventStore):
         *,
         event_types=None,
         limit=500,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="DbRunEventStore.list_events")
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.list_events")
         stmt = select(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.run_id == run_id)
-        if resolved_owner_id is not None:
-            stmt = stmt.where(RunEventRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
         if event_types:
             stmt = stmt.where(RunEventRow.event_type.in_(event_types))
         stmt = stmt.order_by(RunEventRow.seq.asc()).limit(limit)
@@ -199,12 +205,12 @@ class DbRunEventStore(RunEventStore):
         thread_id,
         run_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="DbRunEventStore.list_messages_by_run")
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.list_messages_by_run")
         stmt = select(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.run_id == run_id, RunEventRow.category == "message")
-        if resolved_owner_id is not None:
-            stmt = stmt.where(RunEventRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
         stmt = stmt.order_by(RunEventRow.seq.asc())
         async with self._sf() as session:
             result = await session.execute(stmt)
@@ -214,12 +220,12 @@ class DbRunEventStore(RunEventStore):
         self,
         thread_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="DbRunEventStore.count_messages")
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.count_messages")
         stmt = select(func.count()).select_from(RunEventRow).where(RunEventRow.thread_id == thread_id, RunEventRow.category == "message")
-        if resolved_owner_id is not None:
-            stmt = stmt.where(RunEventRow.owner_id == resolved_owner_id)
+        if resolved_user_id is not None:
+            stmt = stmt.where(RunEventRow.user_id == resolved_user_id)
         async with self._sf() as session:
             return await session.scalar(stmt) or 0
 
@@ -227,13 +233,13 @@ class DbRunEventStore(RunEventStore):
         self,
         thread_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="DbRunEventStore.delete_by_thread")
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.delete_by_thread")
         async with self._sf() as session:
             count_conditions = [RunEventRow.thread_id == thread_id]
-            if resolved_owner_id is not None:
-                count_conditions.append(RunEventRow.owner_id == resolved_owner_id)
+            if resolved_user_id is not None:
+                count_conditions.append(RunEventRow.user_id == resolved_user_id)
             count_stmt = select(func.count()).select_from(RunEventRow).where(*count_conditions)
             count = await session.scalar(count_stmt) or 0
             if count > 0:
@@ -246,13 +252,13 @@ class DbRunEventStore(RunEventStore):
         thread_id,
         run_id,
         *,
-        owner_id: str | None | _AutoSentinel = AUTO,
+        user_id: str | None | _AutoSentinel = AUTO,
     ):
-        resolved_owner_id = resolve_owner_id(owner_id, method_name="DbRunEventStore.delete_by_run")
+        resolved_user_id = resolve_user_id(user_id, method_name="DbRunEventStore.delete_by_run")
         async with self._sf() as session:
             count_conditions = [RunEventRow.thread_id == thread_id, RunEventRow.run_id == run_id]
-            if resolved_owner_id is not None:
-                count_conditions.append(RunEventRow.owner_id == resolved_owner_id)
+            if resolved_user_id is not None:
+                count_conditions.append(RunEventRow.user_id == resolved_user_id)
             count_stmt = select(func.count()).select_from(RunEventRow).where(*count_conditions)
             count = await session.scalar(count_stmt) or 0
             if count > 0:

backend/packages/harness/deerflow/runtime/journal.py

@@ -50,6 +50,7 @@ class RunJournal(BaseCallbackHandler):
 
         # Write buffer
         self._buffer: list[dict] = []
+        self._pending_flush_tasks: set[asyncio.Task[None]] = set()
 
         # Token accumulators
         self._total_input_tokens = 0
@@ -245,6 +246,19 @@ class RunJournal(BaseCallbackHandler):
 
     def on_tool_end(self, output: Any, *, run_id: UUID, **kwargs: Any) -> None:
         from langchain_core.messages import ToolMessage
+        from langgraph.types import Command
+
+        # Tools that update graph state return a ``Command`` (e.g.
+        # ``present_files``). LangGraph later unwraps the inner ToolMessage
+        # into checkpoint state, so to stay checkpoint-aligned we must
+        # extract it here rather than storing ``str(Command(...))``.
+        if isinstance(output, Command):
+            update = getattr(output, "update", None) or {}
+            inner_msgs = update.get("messages") if isinstance(update, dict) else None
+            if isinstance(inner_msgs, list):
+                inner_tool_msg = next((m for m in inner_msgs if isinstance(m, ToolMessage)), None)
+                if inner_tool_msg is not None:
+                    output = inner_tool_msg
 
         # Extract fields from ToolMessage object when LangChain provides one.
         # LangChain's _format_output wraps tool results into a ToolMessage
@@ -381,6 +395,10 @@ class RunJournal(BaseCallbackHandler):
         """
         if not self._buffer:
             return
+        # Skip if a flush is already in flight — avoids concurrent writes
+        # to the same SQLite file from multiple fire-and-forget tasks.
+        if self._pending_flush_tasks:
+            return
         try:
             loop = asyncio.get_running_loop()
         except RuntimeError:
@@ -389,6 +407,7 @@ class RunJournal(BaseCallbackHandler):
         batch = self._buffer.copy()
         self._buffer.clear()
         task = loop.create_task(self._flush_async(batch))
+        self._pending_flush_tasks.add(task)
         task.add_done_callback(self._on_flush_done)
 
     async def _flush_async(self, batch: list[dict]) -> None:
@@ -404,8 +423,8 @@ class RunJournal(BaseCallbackHandler):
             # Return failed events to buffer for retry on next flush
             self._buffer = batch + self._buffer
 
-    @staticmethod
-    def _on_flush_done(task: asyncio.Task) -> None:
+    def _on_flush_done(self, task: asyncio.Task) -> None:
+        self._pending_flush_tasks.discard(task)
         if task.cancelled():
             return
         exc = task.exception()
@@ -450,10 +469,17 @@ class RunJournal(BaseCallbackHandler):
 
     async def flush(self) -> None:
         """Force flush remaining buffer. Called in worker's finally block."""
-        if self._buffer:
-            batch = self._buffer.copy()
-            self._buffer.clear()
-            await self._store.put_batch(batch)
+        if self._pending_flush_tasks:
+            await asyncio.gather(*tuple(self._pending_flush_tasks), return_exceptions=True)
+
+        while self._buffer:
+            batch = self._buffer[: self._flush_threshold]
+            del self._buffer[: self._flush_threshold]
+            try:
+                await self._store.put_batch(batch)
+            except Exception:
+                self._buffer = batch + self._buffer
+                raise
 
     def get_completion_data(self) -> dict:
         """Return accumulated token and message data for run completion."""

backend/packages/harness/deerflow/runtime/runs/store/base.py

@@ -4,8 +4,8 @@ RunManager depends on this interface. Implementations:
 - MemoryRunStore: in-memory dict (development, tests)
 - Future: RunRepository backed by SQLAlchemy ORM
 
-All methods accept an optional owner_id for user isolation.
-When owner_id is None, no user filtering is applied (single-user mode).
+All methods accept an optional user_id for user isolation.
+When user_id is None, no user filtering is applied (single-user mode).
 """
 
 from __future__ import annotations
@@ -22,7 +22,7 @@ class RunStore(abc.ABC):
         *,
         thread_id: str,
         assistant_id: str | None = None,
-        owner_id: str | None = None,
+        user_id: str | None = None,
         status: str = "pending",
         multitask_strategy: str = "reject",
         metadata: dict[str, Any] | None = None,
@@ -42,7 +42,7 @@ class RunStore(abc.ABC):
         self,
         thread_id: str,
         *,
-        owner_id: str | None = None,
+        user_id: str | None = None,
         limit: int = 100,
     ) -> list[dict[str, Any]]:
         pass

backend/packages/harness/deerflow/runtime/runs/store/memory.py

@@ -21,7 +21,7 @@ class MemoryRunStore(RunStore):
         *,
         thread_id,
         assistant_id=None,
-        owner_id=None,
+        user_id=None,
         status="pending",
         multitask_strategy="reject",
         metadata=None,
@@ -35,7 +35,7 @@ class MemoryRunStore(RunStore):
             "run_id": run_id,
             "thread_id": thread_id,
             "assistant_id": assistant_id,
-            "owner_id": owner_id,
+            "user_id": user_id,
             "status": status,
             "multitask_strategy": multitask_strategy,
             "metadata": metadata or {},
@@ -49,8 +49,8 @@ class MemoryRunStore(RunStore):
     async def get(self, run_id):
         return self._runs.get(run_id)
 
-    async def list_by_thread(self, thread_id, *, owner_id=None, limit=100):
-        results = [r for r in self._runs.values() if r["thread_id"] == thread_id and (owner_id is None or r.get("owner_id") == owner_id)]
+    async def list_by_thread(self, thread_id, *, user_id=None, limit=100):
+        results = [r for r in self._runs.values() if r["thread_id"] == thread_id and (user_id is None or r.get("user_id") == user_id)]
         results.sort(key=lambda r: r["created_at"], reverse=True)
         return results[:limit]
 

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

@@ -50,7 +50,7 @@ class RunContext:
     store: Any | None = field(default=None)
     event_store: Any | None = field(default=None)
     run_events_config: Any | None = field(default=None)
-    thread_meta_repo: Any | None = field(default=None)
+    thread_store: Any | None = field(default=None)
     follow_up_to_run_id: str | None = field(default=None)
 
 
@@ -75,7 +75,7 @@ async def run_agent(
     store = ctx.store
     event_store = ctx.event_store
     run_events_config = ctx.run_events_config
-    thread_meta_repo = ctx.thread_meta_repo
+    thread_store = ctx.thread_store
     follow_up_to_run_id = ctx.follow_up_to_run_id
 
     run_id = record.run_id
@@ -85,63 +85,7 @@ 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))
 
     # Track whether "events" was requested but skipped
     if "events" in requested_modes:
@@ -151,6 +95,38 @@ async def run_agent(
         )
 
     try:
+        # Initialize RunJournal + write human_message event.
+        # These are inside the try block so any exception (e.g. a DB
+        # error writing the event) flows through the except/finally
+        # path that publishes an "end" event to the SSE bridge —
+        # otherwise a failure here would leave the stream hanging
+        # with no terminator.
+        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),
+            )
+
+            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))
+
         # 1. Mark running
         await run_manager.set_status(run_id, RunStatus.running)
 
@@ -334,12 +310,15 @@ async def run_agent(
             except Exception:
                 logger.warning("Failed to flush journal for run %s", run_id, exc_info=True)
 
-            # Persist token usage + convenience fields to RunStore
-            completion = journal.get_completion_data()
-            await run_manager.update_run_completion(run_id, status=record.status.value, **completion)
+            try:
+                # Persist token usage + convenience fields to RunStore
+                completion = journal.get_completion_data()
+                await run_manager.update_run_completion(run_id, status=record.status.value, **completion)
+            except Exception:
+                logger.warning("Failed to persist run completion for %s (non-fatal)", run_id, exc_info=True)
 
         # Sync title from checkpoint to threads_meta.display_name
-        if checkpointer is not None:
+        if checkpointer is not None and thread_store is not None:
             try:
                 ckpt_config = {"configurable": {"thread_id": thread_id, "checkpoint_ns": ""}}
                 ckpt_tuple = await checkpointer.aget_tuple(ckpt_config)
@@ -347,16 +326,17 @@ async def run_agent(
                     ckpt = getattr(ckpt_tuple, "checkpoint", {}) or {}
                     title = ckpt.get("channel_values", {}).get("title")
                     if title:
-                        await thread_meta_repo.update_display_name(thread_id, title)
+                        await thread_store.update_display_name(thread_id, title)
             except Exception:
                 logger.debug("Failed to sync title for thread %s (non-fatal)", thread_id)
 
         # Update threads_meta status based on run outcome
-        try:
-            final_status = "idle" if record.status == RunStatus.success else record.status.value
-            await thread_meta_repo.update_status(thread_id, final_status)
-        except Exception:
-            logger.debug("Failed to update thread_meta status for %s (non-fatal)", thread_id)
+        if thread_store is not None:
+            try:
+                final_status = "idle" if record.status == RunStatus.success else record.status.value
+                await thread_store.update_status(thread_id, final_status)
+            except Exception:
+                logger.debug("Failed to update thread_meta status for %s (non-fatal)", thread_id)
 
         await bridge.publish_end(run_id)
         asyncio.create_task(bridge.cleanup(run_id, delay=60))

backend/packages/harness/deerflow/runtime/store/async_provider.py

@@ -91,7 +91,7 @@ async def make_store() -> AsyncIterator[BaseStore]:
     configured checkpointer.
 
     Reads from the same ``checkpointer`` section of *config.yaml* used by
-    :func:`deerflow.agents.checkpointer.async_provider.make_checkpointer` so
+    :func:`deerflow.runtime.checkpointer.async_provider.make_checkpointer` so
     that both singletons always use the same persistence technology::
 
         async with make_store() as store:

backend/packages/harness/deerflow/runtime/stream_bridge/async_provider.py

@@ -1,7 +1,7 @@
 """Async stream bridge factory.
 
 Provides an **async context manager** aligned with
-:func:`deerflow.agents.checkpointer.async_provider.make_checkpointer`.
+:func:`deerflow.runtime.checkpointer.async_provider.make_checkpointer`.
 
 Usage (e.g. FastAPI lifespan)::
 

backend/packages/harness/deerflow/runtime/user_context.py

@@ -1,11 +1,11 @@
-"""Request-scoped user context for owner-based authorization.
+"""Request-scoped user context for user-based authorization.
 
 This module holds a :class:`~contextvars.ContextVar` that the gateway's
 auth middleware sets after a successful authentication. Repository
 methods read the contextvar via a sentinel default parameter, letting
-routers stay free of ``owner_id`` boilerplate.
+routers stay free of ``user_id`` boilerplate.
 
-Three-state semantics for the repository ``owner_id`` parameter (the
+Three-state semantics for the repository ``user_id`` parameter (the
 consumer side of this module lives in ``deerflow.persistence.*``):
 
 - ``_AUTO`` (module-private sentinel, default): read from contextvar;
@@ -91,16 +91,16 @@ def require_current_user() -> CurrentUser:
 
 
 # ---------------------------------------------------------------------------
-# Sentinel-based owner_id resolution
+# Sentinel-based user_id resolution
 # ---------------------------------------------------------------------------
 #
-# Repository methods accept an ``owner_id`` keyword-only argument that
+# Repository methods accept a ``user_id`` keyword-only argument that
 # defaults to ``AUTO``. The three possible values drive distinct
-# behaviours; see the docstring on :func:`resolve_owner_id`.
+# behaviours; see the docstring on :func:`resolve_user_id`.
 
 
 class _AutoSentinel:
-    """Singleton marker meaning 'resolve owner_id from contextvar'."""
+    """Singleton marker meaning 'resolve user_id from contextvar'."""
 
     _instance: _AutoSentinel | None = None
 
@@ -116,12 +116,12 @@ class _AutoSentinel:
 AUTO: Final[_AutoSentinel] = _AutoSentinel()
 
 
-def resolve_owner_id(
+def resolve_user_id(
     value: str | None | _AutoSentinel,
     *,
     method_name: str = "repository method",
 ) -> str | None:
-    """Resolve the owner_id parameter passed to a repository method.
+    """Resolve the user_id parameter passed to a repository method.
 
     Three-state semantics:
 
@@ -131,16 +131,16 @@ def resolve_owner_id(
     - Explicit ``str``: use the provided id verbatim, overriding any
       contextvar value. Useful for tests and admin-override flows.
     - Explicit ``None``: no filter — the repository should skip the
-      owner_id WHERE clause entirely. Reserved for migration scripts
+      user_id WHERE clause entirely. Reserved for migration scripts
       and CLI tools that intentionally bypass isolation.
     """
     if isinstance(value, _AutoSentinel):
         user = _current_user.get()
         if user is None:
-            raise RuntimeError(f"{method_name} called with owner_id=AUTO but no user context is set; pass an explicit owner_id, set the contextvar via auth middleware, or opt out with owner_id=None for migration/CLI paths.")
+            raise RuntimeError(f"{method_name} called with user_id=AUTO but no user context is set; pass an explicit user_id, set the contextvar via auth middleware, or opt out with user_id=None for migration/CLI paths.")
         # Coerce to ``str`` at the boundary: ``User.id`` is typed as
         # ``UUID`` for the API surface, but the persistence layer
-        # stores ``owner_id`` as ``String(64)`` and aiosqlite cannot
+        # stores ``user_id`` as ``String(64)`` and aiosqlite cannot
         # bind a raw UUID object to a VARCHAR column ("type 'UUID' is
         # not supported"). Honour the documented return type here
         # rather than ripple a type change through every caller.

backend/tests/_router_auth_helpers.py

@@ -3,16 +3,16 @@
 The production gateway runs ``AuthMiddleware`` (validates the JWT cookie)
 ahead of every router, plus ``@require_permission(owner_check=True)``
 decorators that read ``request.state.auth`` and call
-``thread_meta_repo.check_access``. Router-level unit tests construct
+``thread_store.check_access``. Router-level unit tests construct
 **bare** FastAPI apps that include only one router — they have neither
-the auth middleware nor a real thread_meta_repo, so the decorators raise
+the auth middleware nor a real thread_store, so the decorators raise
 401 (TestClient path) or ValueError (direct-call path).
 
 This module provides two surfaces:
 
 1. :func:`make_authed_test_app` — wraps ``FastAPI()`` with a tiny
    ``BaseHTTPMiddleware`` that stamps a fake user / AuthContext on every
-   request, plus a permissive ``thread_meta_repo`` mock on
+   request, plus a permissive ``thread_store`` mock on
    ``app.state``. Use from TestClient-based router tests.
 
 2. :func:`call_unwrapped` — invokes the underlying function bypassing
@@ -86,20 +86,20 @@ def make_authed_test_app(
     user_factory: Callable[[], User] | None = None,
     owner_check_passes: bool = True,
 ) -> FastAPI:
-    """Build a FastAPI test app with stub auth + permissive thread_meta_repo.
+    """Build a FastAPI test app with stub auth + permissive thread_store.
 
     Args:
         user_factory: Override the default test user. Must return a fully
             populated :class:`User`. Useful for cross-user isolation tests
             that need a stable id across requests.
-        owner_check_passes: When True (default), ``thread_meta_repo.check_access``
+        owner_check_passes: When True (default), ``thread_store.check_access``
             returns True for every call so ``@require_permission(owner_check=True)``
             never blocks the route under test. Pass False to verify that
             permission failures surface correctly.
 
     Returns:
         A ``FastAPI`` app with the stub middleware installed and
-        ``app.state.thread_meta_repo`` set to a permissive mock. The
+        ``app.state.thread_store`` set to a permissive mock. The
         caller is still responsible for ``app.include_router(...)``.
     """
     factory = user_factory or _make_stub_user
@@ -108,7 +108,7 @@ def make_authed_test_app(
 
     repo = MagicMock()
     repo.check_access = AsyncMock(return_value=owner_check_passes)
-    app.state.thread_meta_repo = repo
+    app.state.thread_store = repo
 
     return app
 

backend/tests/conftest.py

@@ -60,7 +60,7 @@ def provisioner_module():
 # Auto-set user context for every test unless marked no_auto_user
 # ---------------------------------------------------------------------------
 #
-# Repository methods read ``owner_id`` from a contextvar by default
+# Repository methods read ``user_id`` from a contextvar by default
 # (see ``deerflow.runtime.user_context``). Without this fixture, every
 # pre-existing persistence test would raise RuntimeError because the
 # contextvar is unset. The fixture sets a default test user on every

backend/tests/test_checkpointer.py

@@ -6,13 +6,13 @@ from unittest.mock import AsyncMock, MagicMock, patch
 import pytest
 
 import deerflow.config.app_config as app_config_module
-from deerflow.agents.checkpointer import get_checkpointer, reset_checkpointer
 from deerflow.config.checkpointer_config import (
     CheckpointerConfig,
     get_checkpointer_config,
     load_checkpointer_config_from_dict,
     set_checkpointer_config,
 )
+from deerflow.runtime.checkpointer import get_checkpointer, reset_checkpointer
 
 
 @pytest.fixture(autouse=True)
@@ -78,7 +78,7 @@ class TestGetCheckpointer:
         """get_checkpointer should return InMemorySaver when not configured."""
         from langgraph.checkpoint.memory import InMemorySaver
 
-        with patch("deerflow.agents.checkpointer.provider.get_app_config", side_effect=FileNotFoundError):
+        with patch("deerflow.runtime.checkpointer.provider.get_app_config", side_effect=FileNotFoundError):
             cp = get_checkpointer()
         assert cp is not None
         assert isinstance(cp, InMemorySaver)
@@ -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_checkpointer_none_fix.py

@@ -12,14 +12,14 @@ class TestCheckpointerNoneFix:
     @pytest.mark.anyio
     async def test_async_make_checkpointer_returns_in_memory_saver_when_not_configured(self):
         """make_checkpointer should return InMemorySaver when config.checkpointer is None."""
-        from deerflow.agents.checkpointer.async_provider import make_checkpointer
+        from deerflow.runtime.checkpointer.async_provider import make_checkpointer
 
         # Mock get_app_config to return a config with checkpointer=None and database=None
         mock_config = MagicMock()
         mock_config.checkpointer = None
         mock_config.database = None
 
-        with patch("deerflow.agents.checkpointer.async_provider.get_app_config", return_value=mock_config):
+        with patch("deerflow.runtime.checkpointer.async_provider.get_app_config", return_value=mock_config):
             async with make_checkpointer() as checkpointer:
                 # Should return InMemorySaver, not None
                 assert checkpointer is not None
@@ -36,13 +36,13 @@ class TestCheckpointerNoneFix:
 
     def test_sync_checkpointer_context_returns_in_memory_saver_when_not_configured(self):
         """checkpointer_context should return InMemorySaver when config.checkpointer is None."""
-        from deerflow.agents.checkpointer.provider import checkpointer_context
+        from deerflow.runtime.checkpointer.provider import checkpointer_context
 
         # Mock get_app_config to return a config with checkpointer=None
         mock_config = MagicMock()
         mock_config.checkpointer = None
 
-        with patch("deerflow.agents.checkpointer.provider.get_app_config", return_value=mock_config):
+        with patch("deerflow.runtime.checkpointer.provider.get_app_config", return_value=mock_config):
             with checkpointer_context() as checkpointer:
                 # Should return InMemorySaver, not None
                 assert checkpointer is not None

backend/tests/test_client.py

@@ -817,7 +817,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", return_value=[]) as mock_build_middlewares,
             patch("deerflow.client.apply_prompt_template", return_value="prompt") as mock_apply_prompt,
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._agent_name = "custom-agent"
             client._available_skills = {"test_skill"}
@@ -842,7 +842,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=mock_checkpointer),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=mock_checkpointer),
         ):
             client._ensure_agent(config)
 
@@ -867,7 +867,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", side_effect=fake_build_middlewares),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config)
 
@@ -886,7 +886,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=None),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=None),
         ):
             client._ensure_agent(config)
 
@@ -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"
@@ -1844,7 +1844,7 @@ class TestScenarioAgentRecreation:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config_a)
             first_agent = client._agent
@@ -1872,7 +1872,7 @@ class TestScenarioAgentRecreation:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config)
             client._ensure_agent(config)
@@ -1897,7 +1897,7 @@ class TestScenarioAgentRecreation:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config)
             client.reset_agent()

backend/tests/test_ensure_admin.py

@@ -199,12 +199,12 @@ def test_migration_failure_is_non_fatal():
 # ── Section 5.1-5.6 upgrade path: orphan thread migration ────────────────
 
 
-def test_migrate_orphaned_threads_stamps_owner_id_on_unowned_rows():
+def test_migrate_orphaned_threads_stamps_user_id_on_unowned_rows():
     """First boot finds Store-only legacy threads → stamps admin's id.
 
     Validates the **TC-UPG-02 upgrade story**: an operator running main
     (no auth) accumulates threads in the LangGraph Store namespace
-    ``("threads",)`` with no ``metadata.owner_id``. After upgrading to
+    ``("threads",)`` with no ``metadata.user_id``. After upgrading to
     feat/auth-on-2.0-rc, the first ``_ensure_admin_user`` boot should
     rewrite each unowned item with the freshly created admin's id.
     """
@@ -215,7 +215,7 @@ def test_migrate_orphaned_threads_stamps_owner_id_on_unowned_rows():
         SimpleNamespace(key="t1", value={"metadata": {"title": "old-thread-1"}}),
         SimpleNamespace(key="t2", value={"metadata": {"title": "old-thread-2"}}),
         SimpleNamespace(key="t3", value={"metadata": {}}),
-        SimpleNamespace(key="t4", value={"metadata": {"owner_id": "someone-else", "title": "preserved"}}),
+        SimpleNamespace(key="t4", value={"metadata": {"user_id": "someone-else", "title": "preserved"}}),
     ]
     store = AsyncMock()
     # asearch returns the entire batch on first call, then an empty page
@@ -235,11 +235,11 @@ def test_migrate_orphaned_threads_stamps_owner_id_on_unowned_rows():
     assert len(aput_calls) == 3
     rewritten_keys = {call[1] for call in aput_calls}
     assert rewritten_keys == {"t1", "t2", "t3"}
-    # Each rewrite carries the new owner_id; titles preserved where present.
+    # Each rewrite carries the new user_id; titles preserved where present.
     by_key = {call[1]: call[2] for call in aput_calls}
-    assert by_key["t1"]["metadata"]["owner_id"] == "admin-id-42"
+    assert by_key["t1"]["metadata"]["user_id"] == "admin-id-42"
     assert by_key["t1"]["metadata"]["title"] == "old-thread-1"
-    assert by_key["t3"]["metadata"]["owner_id"] == "admin-id-42"
+    assert by_key["t3"]["metadata"]["user_id"] == "admin-id-42"
     # The pre-owned item must NOT have been rewritten.
     assert "t4" not in rewritten_keys
 

backend/tests/test_feedback.py

@@ -60,8 +60,8 @@ class TestFeedbackRepository:
     @pytest.mark.anyio
     async def test_create_with_owner(self, tmp_path):
         repo = await _make_feedback_repo(tmp_path)
-        record = await repo.create(run_id="r1", thread_id="t1", rating=1, owner_id="user-1")
-        assert record["owner_id"] == "user-1"
+        record = await repo.create(run_id="r1", thread_id="t1", rating=1, user_id="user-1")
+        assert record["user_id"] == "user-1"
         await _cleanup()
 
     @pytest.mark.anyio
@@ -97,10 +97,10 @@ class TestFeedbackRepository:
     @pytest.mark.anyio
     async def test_list_by_run(self, tmp_path):
         repo = await _make_feedback_repo(tmp_path)
-        await repo.create(run_id="r1", thread_id="t1", rating=1)
-        await repo.create(run_id="r1", thread_id="t1", rating=-1)
-        await repo.create(run_id="r2", thread_id="t1", rating=1)
-        results = await repo.list_by_run("t1", "r1")
+        await repo.create(run_id="r1", thread_id="t1", rating=1, user_id="user-1")
+        await repo.create(run_id="r1", thread_id="t1", rating=-1, user_id="user-2")
+        await repo.create(run_id="r2", thread_id="t1", rating=1, user_id="user-1")
+        results = await repo.list_by_run("t1", "r1", user_id=None)
         assert len(results) == 2
         assert all(r["run_id"] == "r1" for r in results)
         await _cleanup()
@@ -135,9 +135,9 @@ class TestFeedbackRepository:
     @pytest.mark.anyio
     async def test_aggregate_by_run(self, tmp_path):
         repo = await _make_feedback_repo(tmp_path)
-        await repo.create(run_id="r1", thread_id="t1", rating=1)
-        await repo.create(run_id="r1", thread_id="t1", rating=1)
-        await repo.create(run_id="r1", thread_id="t1", rating=-1)
+        await repo.create(run_id="r1", thread_id="t1", rating=1, user_id="user-1")
+        await repo.create(run_id="r1", thread_id="t1", rating=1, user_id="user-2")
+        await repo.create(run_id="r1", thread_id="t1", rating=-1, user_id="user-3")
         stats = await repo.aggregate_by_run("t1", "r1")
         assert stats["total"] == 3
         assert stats["positive"] == 2
@@ -154,6 +154,80 @@ class TestFeedbackRepository:
         assert stats["negative"] == 0
         await _cleanup()
 
+    @pytest.mark.anyio
+    async def test_upsert_creates_new(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        record = await repo.upsert(run_id="r1", thread_id="t1", rating=1, user_id="u1")
+        assert record["rating"] == 1
+        assert record["feedback_id"]
+        assert record["user_id"] == "u1"
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_upsert_updates_existing(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        first = await repo.upsert(run_id="r1", thread_id="t1", rating=1, user_id="u1")
+        second = await repo.upsert(run_id="r1", thread_id="t1", rating=-1, user_id="u1", comment="changed my mind")
+        assert second["feedback_id"] == first["feedback_id"]
+        assert second["rating"] == -1
+        assert second["comment"] == "changed my mind"
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_upsert_different_users_separate(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        r1 = await repo.upsert(run_id="r1", thread_id="t1", rating=1, user_id="u1")
+        r2 = await repo.upsert(run_id="r1", thread_id="t1", rating=-1, user_id="u2")
+        assert r1["feedback_id"] != r2["feedback_id"]
+        assert r1["rating"] == 1
+        assert r2["rating"] == -1
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_upsert_invalid_rating(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        with pytest.raises(ValueError):
+            await repo.upsert(run_id="r1", thread_id="t1", rating=0, user_id="u1")
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_delete_by_run(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        await repo.upsert(run_id="r1", thread_id="t1", rating=1, user_id="u1")
+        deleted = await repo.delete_by_run(thread_id="t1", run_id="r1", user_id="u1")
+        assert deleted is True
+        results = await repo.list_by_run("t1", "r1", user_id="u1")
+        assert len(results) == 0
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_delete_by_run_nonexistent(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        deleted = await repo.delete_by_run(thread_id="t1", run_id="r1", user_id="u1")
+        assert deleted is False
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_list_by_thread_grouped(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        await repo.upsert(run_id="r1", thread_id="t1", rating=1, user_id="u1")
+        await repo.upsert(run_id="r2", thread_id="t1", rating=-1, user_id="u1")
+        await repo.upsert(run_id="r3", thread_id="t2", rating=1, user_id="u1")
+        grouped = await repo.list_by_thread_grouped("t1", user_id="u1")
+        assert "r1" in grouped
+        assert "r2" in grouped
+        assert "r3" not in grouped
+        assert grouped["r1"]["rating"] == 1
+        assert grouped["r2"]["rating"] == -1
+        await _cleanup()
+
+    @pytest.mark.anyio
+    async def test_list_by_thread_grouped_empty(self, tmp_path):
+        repo = await _make_feedback_repo(tmp_path)
+        grouped = await repo.list_by_thread_grouped("t1", user_id="u1")
+        assert grouped == {}
+        await _cleanup()
+
 
 # -- Follow-up association --
 

backend/tests/test_langgraph_auth.py

@@ -175,46 +175,46 @@ def _make_ctx(user_id):
 def test_filter_injects_user_id():
     value = {}
     asyncio.run(add_owner_filter(_make_ctx("user-a"), value))
-    assert value["metadata"]["owner_id"] == "user-a"
+    assert value["metadata"]["user_id"] == "user-a"
 
 
 def test_filter_preserves_existing_metadata():
     value = {"metadata": {"title": "hello"}}
     asyncio.run(add_owner_filter(_make_ctx("user-a"), value))
-    assert value["metadata"]["owner_id"] == "user-a"
+    assert value["metadata"]["user_id"] == "user-a"
     assert value["metadata"]["title"] == "hello"
 
 
 def test_filter_returns_user_id_dict():
     result = asyncio.run(add_owner_filter(_make_ctx("user-x"), {}))
-    assert result == {"owner_id": "user-x"}
+    assert result == {"user_id": "user-x"}
 
 
 def test_filter_read_write_consistency():
     value = {}
     filter_dict = asyncio.run(add_owner_filter(_make_ctx("user-1"), value))
-    assert value["metadata"]["owner_id"] == filter_dict["owner_id"]
+    assert value["metadata"]["user_id"] == filter_dict["user_id"]
 
 
 def test_different_users_different_filters():
     f_a = asyncio.run(add_owner_filter(_make_ctx("a"), {}))
     f_b = asyncio.run(add_owner_filter(_make_ctx("b"), {}))
-    assert f_a["owner_id"] != f_b["owner_id"]
+    assert f_a["user_id"] != f_b["user_id"]
 
 
 def test_filter_overrides_conflicting_user_id():
     """If value already has a different user_id in metadata, it gets overwritten."""
-    value = {"metadata": {"owner_id": "attacker"}}
+    value = {"metadata": {"user_id": "attacker"}}
     asyncio.run(add_owner_filter(_make_ctx("real-owner"), value))
-    assert value["metadata"]["owner_id"] == "real-owner"
+    assert value["metadata"]["user_id"] == "real-owner"
 
 
 def test_filter_with_empty_metadata():
     """Explicit empty metadata dict is fine."""
     value = {"metadata": {}}
     result = asyncio.run(add_owner_filter(_make_ctx("user-z"), value))
-    assert value["metadata"]["owner_id"] == "user-z"
-    assert result == {"owner_id": "user-z"}
+    assert value["metadata"]["user_id"] == "user-z"
+    assert result == {"user_id": "user-z"}
 
 
 # ── Gateway parity ───────────────────────────────────────────────────────

backend/tests/test_memory_thread_meta_isolation.py

@@ -0,0 +1,156 @@
+"""Owner isolation tests for MemoryThreadMetaStore.
+
+Mirrors the SQL-backed tests in test_owner_isolation.py but exercises
+the in-memory LangGraph Store backend used when database.backend=memory.
+"""
+
+from __future__ import annotations
+
+from types import SimpleNamespace
+
+import pytest
+from langgraph.store.memory import InMemoryStore
+
+from deerflow.persistence.thread_meta.memory import MemoryThreadMetaStore
+from deerflow.runtime.user_context import reset_current_user, set_current_user
+
+USER_A = SimpleNamespace(id="user-a", email="a@test.local")
+USER_B = SimpleNamespace(id="user-b", email="b@test.local")
+
+
+def _as_user(user):
+    class _Ctx:
+        def __enter__(self):
+            self._token = set_current_user(user)
+            return user
+
+        def __exit__(self, *exc):
+            reset_current_user(self._token)
+
+    return _Ctx()
+
+
+@pytest.fixture
+def store():
+    return MemoryThreadMetaStore(InMemoryStore())
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_search_isolation(store):
+    """search() returns only threads owned by the current user."""
+    with _as_user(USER_A):
+        await store.create("t-alpha", display_name="A's thread")
+    with _as_user(USER_B):
+        await store.create("t-beta", display_name="B's thread")
+
+    with _as_user(USER_A):
+        results = await store.search()
+        assert [r["thread_id"] for r in results] == ["t-alpha"]
+
+    with _as_user(USER_B):
+        results = await store.search()
+        assert [r["thread_id"] for r in results] == ["t-beta"]
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_get_isolation(store):
+    """get() returns None for threads owned by another user."""
+    with _as_user(USER_A):
+        await store.create("t-alpha", display_name="A's thread")
+
+    with _as_user(USER_B):
+        assert await store.get("t-alpha") is None
+
+    with _as_user(USER_A):
+        result = await store.get("t-alpha")
+        assert result is not None
+        assert result["display_name"] == "A's thread"
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_update_display_name_denied(store):
+    """User B cannot rename User A's thread."""
+    with _as_user(USER_A):
+        await store.create("t-alpha", display_name="original")
+
+    with _as_user(USER_B):
+        await store.update_display_name("t-alpha", "hacked")
+
+    with _as_user(USER_A):
+        row = await store.get("t-alpha")
+        assert row is not None
+        assert row["display_name"] == "original"
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_update_status_denied(store):
+    """User B cannot change status of User A's thread."""
+    with _as_user(USER_A):
+        await store.create("t-alpha")
+
+    with _as_user(USER_B):
+        await store.update_status("t-alpha", "error")
+
+    with _as_user(USER_A):
+        row = await store.get("t-alpha")
+        assert row is not None
+        assert row["status"] == "idle"
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_update_metadata_denied(store):
+    """User B cannot modify metadata of User A's thread."""
+    with _as_user(USER_A):
+        await store.create("t-alpha", metadata={"key": "original"})
+
+    with _as_user(USER_B):
+        await store.update_metadata("t-alpha", {"key": "hacked"})
+
+    with _as_user(USER_A):
+        row = await store.get("t-alpha")
+        assert row is not None
+        assert row["metadata"]["key"] == "original"
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_delete_denied(store):
+    """User B cannot delete User A's thread."""
+    with _as_user(USER_A):
+        await store.create("t-alpha")
+
+    with _as_user(USER_B):
+        await store.delete("t-alpha")
+
+    with _as_user(USER_A):
+        row = await store.get("t-alpha")
+        assert row is not None
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_no_context_raises(store):
+    """Calling methods without user context raises RuntimeError."""
+    with pytest.raises(RuntimeError, match="no user context is set"):
+        await store.search()
+
+
+@pytest.mark.anyio
+@pytest.mark.no_auto_user
+async def test_explicit_none_bypasses_filter(store):
+    """user_id=None bypasses isolation (migration/CLI escape hatch)."""
+    with _as_user(USER_A):
+        await store.create("t-alpha")
+    with _as_user(USER_B):
+        await store.create("t-beta")
+
+    all_rows = await store.search(user_id=None)
+    assert {r["thread_id"] for r in all_rows} == {"t-alpha", "t-beta"}
+
+    row = await store.get("t-alpha", user_id=None)
+    assert row is not None

backend/tests/test_owner_isolation.py

@@ -9,8 +9,8 @@ These tests bypass the HTTP layer and exercise the storage-layer
 owner filter directly by switching the ``user_context`` contextvar
 between two users. The safety property under test is:
 
-  After a repository write with owner_id=A, a subsequent read with
-  owner_id=B must not return the row, and vice versa.
+  After a repository write with user_id=A, a subsequent read with
+  user_id=B must not return the row, and vice versa.
 
 The HTTP layer is covered by test_auth_middleware.py, which proves
 that a request cookie reaches the ``set_current_user`` call. Together
@@ -431,13 +431,13 @@ async def test_repository_without_context_raises(tmp_path):
         await cleanup()
 
 
-# ── Escape hatch: explicit owner_id=None bypasses filter (for migration) ──
+# ── Escape hatch: explicit user_id=None bypasses filter (for migration) ──
 
 
 @pytest.mark.anyio
 @pytest.mark.no_auto_user
 async def test_explicit_none_bypasses_filter(tmp_path):
-    """Migration scripts pass owner_id=None to see all rows regardless of owner."""
+    """Migration scripts pass user_id=None to see all rows regardless of owner."""
     from deerflow.persistence.engine import get_session_factory
     from deerflow.persistence.thread_meta import ThreadMetaRepository
 
@@ -452,14 +452,14 @@ async def test_explicit_none_bypasses_filter(tmp_path):
             await repo.create("t-beta")
 
         # Migration-style read: no contextvar, explicit None bypass.
-        all_rows = await repo.search(owner_id=None)
+        all_rows = await repo.search(user_id=None)
         thread_ids = {r["thread_id"] for r in all_rows}
         assert thread_ids == {"t-alpha", "t-beta"}
 
         # Explicit get with None does not apply the filter either.
-        row_a = await repo.get("t-alpha", owner_id=None)
+        row_a = await repo.get("t-alpha", user_id=None)
         assert row_a is not None
-        row_b = await repo.get("t-beta", owner_id=None)
+        row_b = await repo.get("t-beta", user_id=None)
         assert row_b is not None
     finally:
         await cleanup()

backend/tests/test_persistence_scaffold.py

@@ -2,7 +2,7 @@
 
 Tests:
 1. DatabaseConfig property derivation (paths, URLs)
-2. MemoryRunStore CRUD + owner_id filtering
+2. MemoryRunStore CRUD + user_id filtering
 3. Base.to_dict() via inspect mixin
 4. Engine init/close lifecycle (memory + SQLite)
 5. Postgres missing-dep error message
@@ -24,18 +24,19 @@ class TestDatabaseConfig:
         assert c.backend == "memory"
         assert c.pool_size == 5
 
-    def test_sqlite_paths_are_different(self):
+    def test_sqlite_paths_unified(self):
         c = DatabaseConfig(backend="sqlite", sqlite_dir="./mydata")
-        assert c.checkpointer_sqlite_path.endswith("checkpoints.db")
-        assert c.app_sqlite_path.endswith("app.db")
-        assert "mydata" in c.checkpointer_sqlite_path
-        assert c.checkpointer_sqlite_path != c.app_sqlite_path
+        assert c.sqlite_path.endswith("deerflow.db")
+        assert "mydata" in c.sqlite_path
+        # Backward-compatible aliases point to the same file
+        assert c.checkpointer_sqlite_path == c.sqlite_path
+        assert c.app_sqlite_path == c.sqlite_path
 
     def test_app_sqlalchemy_url_sqlite(self):
         c = DatabaseConfig(backend="sqlite", sqlite_dir="./data")
         url = c.app_sqlalchemy_url
         assert url.startswith("sqlite+aiosqlite:///")
-        assert "app.db" in url
+        assert "deerflow.db" in url
 
     def test_app_sqlalchemy_url_postgres(self):
         c = DatabaseConfig(
@@ -105,17 +106,17 @@ class TestMemoryRunStore:
 
     @pytest.mark.anyio
     async def test_list_by_thread_owner_filter(self, store):
-        await store.put("r1", thread_id="t1", owner_id="alice")
-        await store.put("r2", thread_id="t1", owner_id="bob")
-        rows = await store.list_by_thread("t1", owner_id="alice")
+        await store.put("r1", thread_id="t1", user_id="alice")
+        await store.put("r2", thread_id="t1", user_id="bob")
+        rows = await store.list_by_thread("t1", user_id="alice")
         assert len(rows) == 1
-        assert rows[0]["owner_id"] == "alice"
+        assert rows[0]["user_id"] == "alice"
 
     @pytest.mark.anyio
     async def test_owner_none_returns_all(self, store):
-        await store.put("r1", thread_id="t1", owner_id="alice")
-        await store.put("r2", thread_id="t1", owner_id="bob")
-        rows = await store.list_by_thread("t1", owner_id=None)
+        await store.put("r1", thread_id="t1", user_id="alice")
+        await store.put("r2", thread_id="t1", user_id="bob")
+        rows = await store.list_by_thread("t1", user_id=None)
         assert len(rows) == 2
 
     @pytest.mark.anyio

backend/tests/test_run_journal.py

@@ -709,6 +709,81 @@ class TestToolResultMessage:
         assert tool_end["metadata"]["tool_call_id"] == "call_from_obj"
         assert tool_end["metadata"]["tool_name"] == "web_search"
 
+    @pytest.mark.anyio
+    async def test_tool_invoke_end_to_end_unwraps_command(self, journal_setup):
+        """End-to-end: invoke a real LangChain tool that returns Command(update={'messages':[ToolMessage]}).
+
+        This goes through the real LangChain callback path (tool.invoke -> CallbackManager
+        -> on_tool_start/on_tool_end), which is what the production agent uses. Mirrors
+        the ``present_files`` tool shape exactly.
+        """
+        from langchain_core.callbacks import CallbackManager
+        from langchain_core.messages import ToolMessage
+        from langchain_core.tools import tool
+        from langgraph.types import Command
+
+        j, store = journal_setup
+
+        @tool
+        def fake_present_files(filepaths: list[str]) -> Command:
+            """Fake present_files that returns a Command with an inner ToolMessage."""
+            return Command(
+                update={
+                    "artifacts": filepaths,
+                    "messages": [ToolMessage("Successfully presented files", tool_call_id="tc_123")],
+                },
+            )
+
+        # Real LangChain callback dispatch (matches production agent path)
+        cm = CallbackManager(handlers=[j])
+        fake_present_files.invoke(
+            {"filepaths": ["/mnt/user-data/outputs/report.md"]},
+            config={"callbacks": cm, "run_id": uuid4()},
+        )
+        await j.flush()
+
+        messages = await store.list_messages("t1")
+        assert len(messages) == 1, f"expected 1 message event, got {len(messages)}: {messages}"
+        content = messages[0]["content"]
+        assert content["type"] == "tool"
+        # CRITICAL: must be the inner ToolMessage text, not str(Command(...))
+        assert content["content"] == "Successfully presented files", (
+            f"Command unwrap failed; stored content = {content['content']!r}"
+        )
+        assert "Command(update=" not in str(content["content"])
+
+    @pytest.mark.anyio
+    async def test_tool_end_unwraps_command_with_inner_tool_message(self, journal_setup):
+        """Tools like ``present_files`` return Command(update={'messages': [ToolMessage(...)]}).
+
+        LangGraph unwraps the inner ToolMessage into checkpoint state, so the
+        event store must do the same — otherwise it captures ``str(Command(...))``
+        and the /history response diverges from the real rendered message.
+        """
+        from langchain_core.messages import ToolMessage
+        from langgraph.types import Command
+
+        j, store = journal_setup
+        run_id = uuid4()
+        inner = ToolMessage(
+            content="Successfully presented files",
+            tool_call_id="call_present",
+            name="present_files",
+            status="success",
+        )
+        cmd = Command(update={"artifacts": ["/mnt/user-data/outputs/report.md"], "messages": [inner]})
+        j.on_tool_end(cmd, run_id=run_id)
+        await j.flush()
+
+        messages = await store.list_messages("t1")
+        assert len(messages) == 1
+        content = messages[0]["content"]
+        assert content["type"] == "tool"
+        assert content["content"] == "Successfully presented files"
+        assert content["tool_call_id"] == "call_present"
+        assert content["name"] == "present_files"
+        assert "Command(update=" not in str(content["content"])
+
     @pytest.mark.anyio
     async def test_tool_message_object_overrides_kwargs(self, journal_setup):
         """ToolMessage object fields take priority over kwargs."""

backend/tests/test_run_repository.py

@@ -73,11 +73,11 @@ class TestRunRepository:
     @pytest.mark.anyio
     async def test_list_by_thread_owner_filter(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        await repo.put("r1", thread_id="t1", owner_id="alice")
-        await repo.put("r2", thread_id="t1", owner_id="bob")
-        rows = await repo.list_by_thread("t1", owner_id="alice")
+        await repo.put("r1", thread_id="t1", user_id="alice")
+        await repo.put("r2", thread_id="t1", user_id="bob")
+        rows = await repo.list_by_thread("t1", user_id="alice")
         assert len(rows) == 1
-        assert rows[0]["owner_id"] == "alice"
+        assert rows[0]["user_id"] == "alice"
         await _cleanup()
 
     @pytest.mark.anyio
@@ -189,8 +189,8 @@ class TestRunRepository:
     @pytest.mark.anyio
     async def test_owner_none_returns_all(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        await repo.put("r1", thread_id="t1", owner_id="alice")
-        await repo.put("r2", thread_id="t1", owner_id="bob")
-        rows = await repo.list_by_thread("t1", owner_id=None)
+        await repo.put("r1", thread_id="t1", user_id="alice")
+        await repo.put("r2", thread_id="t1", user_id="bob")
+        rows = await repo.list_by_thread("t1", user_id=None)
         assert len(rows) == 2
         await _cleanup()

backend/tests/test_suggestions_router.py

@@ -47,7 +47,7 @@ def test_generate_suggestions_parses_and_limits(monkeypatch):
     monkeypatch.setattr(suggestions, "create_chat_model", lambda **kwargs: fake_model)
 
     # Bypass the require_permission decorator (which needs request +
-    # thread_meta_repo) — these tests cover the parsing logic.
+    # thread_store) — these tests cover the parsing logic.
     result = asyncio.run(suggestions.generate_suggestions.__wrapped__("t1", req, request=None))
 
     assert result.suggestions == ["Q1", "Q2", "Q3"]
@@ -67,7 +67,7 @@ def test_generate_suggestions_parses_list_block_content(monkeypatch):
     monkeypatch.setattr(suggestions, "create_chat_model", lambda **kwargs: fake_model)
 
     # Bypass the require_permission decorator (which needs request +
-    # thread_meta_repo) — these tests cover the parsing logic.
+    # thread_store) — these tests cover the parsing logic.
     result = asyncio.run(suggestions.generate_suggestions.__wrapped__("t1", req, request=None))
 
     assert result.suggestions == ["Q1", "Q2"]
@@ -87,7 +87,7 @@ def test_generate_suggestions_parses_output_text_block_content(monkeypatch):
     monkeypatch.setattr(suggestions, "create_chat_model", lambda **kwargs: fake_model)
 
     # Bypass the require_permission decorator (which needs request +
-    # thread_meta_repo) — these tests cover the parsing logic.
+    # thread_store) — these tests cover the parsing logic.
     result = asyncio.run(suggestions.generate_suggestions.__wrapped__("t1", req, request=None))
 
     assert result.suggestions == ["Q1", "Q2"]
@@ -104,7 +104,7 @@ def test_generate_suggestions_returns_empty_on_model_error(monkeypatch):
     monkeypatch.setattr(suggestions, "create_chat_model", lambda **kwargs: fake_model)
 
     # Bypass the require_permission decorator (which needs request +
-    # thread_meta_repo) — these tests cover the parsing logic.
+    # thread_store) — these tests cover the parsing logic.
     result = asyncio.run(suggestions.generate_suggestions.__wrapped__("t1", req, request=None))
 
     assert result.suggestions == []

backend/tests/test_thread_meta_repo.py

@@ -43,8 +43,8 @@ class TestThreadMetaRepository:
     @pytest.mark.anyio
     async def test_create_with_owner_and_display_name(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        record = await repo.create("t1", owner_id="user1", display_name="My Thread")
-        assert record["owner_id"] == "user1"
+        record = await repo.create("t1", user_id="user1", display_name="My Thread")
+        assert record["user_id"] == "user1"
         assert record["display_name"] == "My Thread"
         await _cleanup()
 
@@ -61,26 +61,6 @@ class TestThreadMetaRepository:
         assert await repo.get("nonexistent") is None
         await _cleanup()
 
-    @pytest.mark.anyio
-    async def test_list_by_owner(self, tmp_path):
-        repo = await _make_repo(tmp_path)
-        await repo.create("t1", owner_id="user1")
-        await repo.create("t2", owner_id="user1")
-        await repo.create("t3", owner_id="user2")
-        results = await repo.list_by_owner("user1")
-        assert len(results) == 2
-        assert all(r["owner_id"] == "user1" for r in results)
-        await _cleanup()
-
-    @pytest.mark.anyio
-    async def test_list_by_owner_with_limit_and_offset(self, tmp_path):
-        repo = await _make_repo(tmp_path)
-        for i in range(5):
-            await repo.create(f"t{i}", owner_id="user1")
-        results = await repo.list_by_owner("user1", limit=2, offset=1)
-        assert len(results) == 2
-        await _cleanup()
-
     @pytest.mark.anyio
     async def test_check_access_no_record_allows(self, tmp_path):
         repo = await _make_repo(tmp_path)
@@ -90,23 +70,23 @@ class TestThreadMetaRepository:
     @pytest.mark.anyio
     async def test_check_access_owner_matches(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        await repo.create("t1", owner_id="user1")
+        await repo.create("t1", user_id="user1")
         assert await repo.check_access("t1", "user1") is True
         await _cleanup()
 
     @pytest.mark.anyio
     async def test_check_access_owner_mismatch(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        await repo.create("t1", owner_id="user1")
+        await repo.create("t1", user_id="user1")
         assert await repo.check_access("t1", "user2") is False
         await _cleanup()
 
     @pytest.mark.anyio
     async def test_check_access_no_owner_allows_all(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        # Explicit owner_id=None to bypass the new AUTO default that
+        # Explicit user_id=None to bypass the new AUTO default that
         # would otherwise pick up the test user from the autouse fixture.
-        await repo.create("t1", owner_id=None)
+        await repo.create("t1", user_id=None)
         assert await repo.check_access("t1", "anyone") is True
         await _cleanup()
 
@@ -125,27 +105,27 @@ class TestThreadMetaRepository:
     @pytest.mark.anyio
     async def test_check_access_strict_owner_match_allowed(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        await repo.create("t1", owner_id="user1")
+        await repo.create("t1", user_id="user1")
         assert await repo.check_access("t1", "user1", require_existing=True) is True
         await _cleanup()
 
     @pytest.mark.anyio
     async def test_check_access_strict_owner_mismatch_denied(self, tmp_path):
         repo = await _make_repo(tmp_path)
-        await repo.create("t1", owner_id="user1")
+        await repo.create("t1", user_id="user1")
         assert await repo.check_access("t1", "user2", require_existing=True) is False
         await _cleanup()
 
     @pytest.mark.anyio
     async def test_check_access_strict_null_owner_still_allowed(self, tmp_path):
-        """Even in strict mode, a row with NULL owner_id stays shared.
+        """Even in strict mode, a row with NULL user_id stays shared.
 
         The strict flag tightens the *missing row* case, not the *shared
         row* case — legacy pre-auth rows that survived a clean migration
         without an owner are still everyone's.
         """
         repo = await _make_repo(tmp_path)
-        await repo.create("t1", owner_id=None)
+        await repo.create("t1", user_id=None)
         assert await repo.check_access("t1", "anyone", require_existing=True) is True
         await _cleanup()
 

backend/tests/test_thread_state_event_store.py

@@ -0,0 +1,439 @@
+"""Tests for event-store-backed message loading in thread state/history endpoints.
+
+Covers the helper functions added to ``app/gateway/routers/threads.py``:
+
+- ``_sanitize_legacy_command_repr`` — extracts inner ToolMessage text from
+  legacy ``str(Command(...))`` strings captured before the ``journal.py``
+  fix for state-updating tools like ``present_files``.
+- ``_get_event_store_messages`` — loads the full message stream with full
+  pagination, copy-on-read id patching, legacy Command sanitization, and
+  a clean fallback to ``None`` when the event store is unavailable.
+"""
+
+from __future__ import annotations
+
+import uuid
+from types import SimpleNamespace
+from typing import Any
+
+import pytest
+
+from app.gateway.routers.threads import (
+    _get_event_store_messages,
+    _sanitize_legacy_command_repr,
+)
+from deerflow.runtime.events.store.memory import MemoryRunEventStore
+
+
+@pytest.fixture()
+def event_store() -> MemoryRunEventStore:
+    return MemoryRunEventStore()
+
+
+class _FakeFeedbackRepo:
+    """Minimal ``FeedbackRepository`` stand-in that returns a configured map."""
+
+    def __init__(self, by_run: dict[str, dict] | None = None) -> None:
+        self._by_run = by_run or {}
+
+    async def list_by_thread_grouped(self, thread_id: str, *, user_id: str | None) -> dict[str, dict]:
+        return dict(self._by_run)
+
+
+def _make_request(
+    event_store: MemoryRunEventStore,
+    feedback_repo: _FakeFeedbackRepo | None = None,
+) -> Any:
+    """Build a minimal FastAPI-like Request object.
+
+    ``get_run_event_store(request)`` reads ``request.app.state.run_event_store``.
+    ``get_feedback_repo(request)`` reads ``request.app.state.feedback_repo``.
+    ``get_current_user`` is monkey-patched separately in tests that need it.
+    """
+    state = SimpleNamespace(
+        run_event_store=event_store,
+        feedback_repo=feedback_repo or _FakeFeedbackRepo(),
+    )
+    app = SimpleNamespace(state=state)
+    return SimpleNamespace(app=app)
+
+
+@pytest.fixture(autouse=True)
+def _stub_current_user(monkeypatch):
+    """Stub out ``get_current_user`` so tests don't need real auth context."""
+    import app.gateway.routers.threads as threads_mod
+
+    async def _fake(_request):
+        return None
+
+    monkeypatch.setattr(threads_mod, "get_current_user", _fake)
+
+
+async def _seed_simple_run(store: MemoryRunEventStore, thread_id: str, run_id: str) -> None:
+    """Seed one run: human + ai_tool_call + tool_result + final ai_message, plus a trace."""
+    await store.put(
+        thread_id=thread_id, run_id=run_id,
+        event_type="human_message", category="message",
+        content={
+            "type": "human", "id": None,
+            "content": [{"type": "text", "text": "hello"}],
+            "additional_kwargs": {}, "response_metadata": {}, "name": None,
+        },
+    )
+    await store.put(
+        thread_id=thread_id, run_id=run_id,
+        event_type="ai_tool_call", category="message",
+        content={
+            "type": "ai", "id": "lc_run--tc1",
+            "content": "",
+            "tool_calls": [{"name": "search", "args": {"q": "x"}, "id": "call_1", "type": "tool_call"}],
+            "invalid_tool_calls": [],
+            "additional_kwargs": {}, "response_metadata": {}, "name": None,
+            "usage_metadata": {"input_tokens": 10, "output_tokens": 5, "total_tokens": 15},
+        },
+    )
+    await store.put(
+        thread_id=thread_id, run_id=run_id,
+        event_type="tool_result", category="message",
+        content={
+            "type": "tool", "id": None,
+            "content": "results",
+            "tool_call_id": "call_1", "name": "search",
+            "artifact": None, "status": "success",
+            "additional_kwargs": {}, "response_metadata": {},
+        },
+    )
+    await store.put(
+        thread_id=thread_id, run_id=run_id,
+        event_type="ai_message", category="message",
+        content={
+            "type": "ai", "id": "lc_run--final1",
+            "content": "done",
+            "tool_calls": [], "invalid_tool_calls": [],
+            "additional_kwargs": {}, "response_metadata": {"finish_reason": "stop"}, "name": None,
+            "usage_metadata": {"input_tokens": 20, "output_tokens": 10, "total_tokens": 30},
+        },
+    )
+    # Non-message trace — must be filtered out.
+    await store.put(
+        thread_id=thread_id, run_id=run_id,
+        event_type="llm_request", category="trace",
+        content={"model": "test"},
+    )
+
+
+class TestSanitizeLegacyCommandRepr:
+    def test_passthrough_non_string(self):
+        assert _sanitize_legacy_command_repr(None) is None
+        assert _sanitize_legacy_command_repr(42) == 42
+        assert _sanitize_legacy_command_repr([{"type": "text", "text": "x"}]) == [{"type": "text", "text": "x"}]
+
+    def test_passthrough_plain_string(self):
+        assert _sanitize_legacy_command_repr("Successfully presented files") == "Successfully presented files"
+        assert _sanitize_legacy_command_repr("") == ""
+
+    def test_extracts_inner_content_single_quotes(self):
+        legacy = (
+            "Command(update={'artifacts': ['/mnt/user-data/outputs/report.md'], "
+            "'messages': [ToolMessage(content='Successfully presented files', "
+            "tool_call_id='call_abc')]})"
+        )
+        assert _sanitize_legacy_command_repr(legacy) == "Successfully presented files"
+
+    def test_extracts_inner_content_double_quotes(self):
+        legacy = 'Command(update={"messages": [ToolMessage(content="ok", tool_call_id="x")]})'
+        assert _sanitize_legacy_command_repr(legacy) == "ok"
+
+    def test_unparseable_command_returns_original(self):
+        legacy = "Command(update={'something_else': 1})"
+        assert _sanitize_legacy_command_repr(legacy) == legacy
+
+
+class TestGetEventStoreMessages:
+    @pytest.mark.anyio
+    async def test_returns_none_when_store_empty(self, event_store):
+        request = _make_request(event_store)
+        assert await _get_event_store_messages(request, "t_missing") is None
+
+    @pytest.mark.anyio
+    async def test_extracts_all_message_types_in_order(self, event_store):
+        await _seed_simple_run(event_store, "t1", "r1")
+        request = _make_request(event_store)
+        messages = await _get_event_store_messages(request, "t1")
+        assert messages is not None
+        types = [m["type"] for m in messages]
+        assert types == ["human", "ai", "tool", "ai"]
+        # Trace events must not appear
+        for m in messages:
+            assert m.get("type") in {"human", "ai", "tool"}
+
+    @pytest.mark.anyio
+    async def test_null_ids_get_deterministic_uuid5(self, event_store):
+        await _seed_simple_run(event_store, "t1", "r1")
+        request = _make_request(event_store)
+        messages = await _get_event_store_messages(request, "t1")
+        assert messages is not None
+
+        # AI messages keep their LLM ids
+        assert messages[1]["id"] == "lc_run--tc1"
+        assert messages[3]["id"] == "lc_run--final1"
+
+        # Human (seq=1) + tool (seq=3) get deterministic uuid5
+        expected_human_id = str(uuid.uuid5(uuid.NAMESPACE_URL, "t1:1"))
+        expected_tool_id = str(uuid.uuid5(uuid.NAMESPACE_URL, "t1:3"))
+        assert messages[0]["id"] == expected_human_id
+        assert messages[2]["id"] == expected_tool_id
+
+        # Re-running produces the same ids (stability across requests)
+        messages2 = await _get_event_store_messages(request, "t1")
+        assert [m["id"] for m in messages2] == [m["id"] for m in messages]
+
+    @pytest.mark.anyio
+    async def test_helper_does_not_mutate_store(self, event_store):
+        """Helper must copy content dicts; the live store must stay unchanged."""
+        await _seed_simple_run(event_store, "t1", "r1")
+        request = _make_request(event_store)
+        _ = await _get_event_store_messages(request, "t1")
+
+        # Raw store records still have id=None for human/tool
+        raw = await event_store.list_messages("t1", limit=500)
+        human = next(e for e in raw if e["content"]["type"] == "human")
+        tool = next(e for e in raw if e["content"]["type"] == "tool")
+        assert human["content"]["id"] is None
+        assert tool["content"]["id"] is None
+
+    @pytest.mark.anyio
+    async def test_legacy_command_repr_sanitized(self, event_store):
+        """A tool_result whose content is a legacy ``str(Command(...))`` is cleaned."""
+        legacy = (
+            "Command(update={'artifacts': ['/mnt/user-data/outputs/x.md'], "
+            "'messages': [ToolMessage(content='Successfully presented files', "
+            "tool_call_id='call_p')]})"
+        )
+        await event_store.put(
+            thread_id="t2", run_id="r1",
+            event_type="tool_result", category="message",
+            content={
+                "type": "tool", "id": None,
+                "content": legacy,
+                "tool_call_id": "call_p", "name": "present_files",
+                "artifact": None, "status": "success",
+                "additional_kwargs": {}, "response_metadata": {},
+            },
+        )
+        request = _make_request(event_store)
+        messages = await _get_event_store_messages(request, "t2")
+        assert messages is not None and len(messages) == 1
+        assert messages[0]["content"] == "Successfully presented files"
+
+    @pytest.mark.anyio
+    async def test_pagination_covers_more_than_one_page(self, event_store, monkeypatch):
+        """Simulate a long thread that exceeds a single page to exercise the loop."""
+        thread_id = "t_long"
+        # Seed 12 human messages
+        for i in range(12):
+            await event_store.put(
+                thread_id=thread_id, run_id="r1",
+                event_type="human_message", category="message",
+                content={
+                    "type": "human", "id": None,
+                    "content": [{"type": "text", "text": f"msg {i}"}],
+                    "additional_kwargs": {}, "response_metadata": {}, "name": None,
+                },
+            )
+
+        # Force small page size to exercise pagination
+        import app.gateway.routers.threads as threads_mod
+        original = threads_mod._get_event_store_messages
+
+        # Monkeypatch MemoryRunEventStore.list_messages to assert it's called with cursor pagination
+        calls: list[dict] = []
+        real_list = event_store.list_messages
+
+        async def spy_list_messages(tid, *, limit=50, before_seq=None, after_seq=None):
+            calls.append({"limit": limit, "after_seq": after_seq})
+            return await real_list(tid, limit=limit, before_seq=before_seq, after_seq=after_seq)
+
+        monkeypatch.setattr(event_store, "list_messages", spy_list_messages)
+
+        request = _make_request(event_store)
+        messages = await original(request, thread_id)
+        assert messages is not None
+        assert len(messages) == 12
+        assert [m["content"][0]["text"] for m in messages] == [f"msg {i}" for i in range(12)]
+        # At least one call was made with after_seq=None (the initial page)
+        assert any(c["after_seq"] is None for c in calls)
+
+    @pytest.mark.anyio
+    async def test_summarize_regression_recovers_pre_summarize_messages(self, event_store):
+        """The exact bug: checkpoint would have only post-summarize messages;
+        event store must surface the original pre-summarize human query."""
+        # Run 1 (pre-summarize)
+        await event_store.put(
+            thread_id="t_sum", run_id="r1",
+            event_type="human_message", category="message",
+            content={
+                "type": "human", "id": None,
+                "content": [{"type": "text", "text": "original question"}],
+                "additional_kwargs": {}, "response_metadata": {}, "name": None,
+            },
+        )
+        await event_store.put(
+            thread_id="t_sum", run_id="r1",
+            event_type="ai_message", category="message",
+            content={
+                "type": "ai", "id": "lc_run--r1",
+                "content": "first answer",
+                "tool_calls": [], "invalid_tool_calls": [],
+                "additional_kwargs": {}, "response_metadata": {}, "name": None,
+                "usage_metadata": {"input_tokens": 0, "output_tokens": 0, "total_tokens": 0},
+            },
+        )
+        # Run 2 (post-summarize — what the checkpoint still has)
+        await event_store.put(
+            thread_id="t_sum", run_id="r2",
+            event_type="human_message", category="message",
+            content={
+                "type": "human", "id": None,
+                "content": [{"type": "text", "text": "follow up"}],
+                "additional_kwargs": {}, "response_metadata": {}, "name": None,
+            },
+        )
+        await event_store.put(
+            thread_id="t_sum", run_id="r2",
+            event_type="ai_message", category="message",
+            content={
+                "type": "ai", "id": "lc_run--r2",
+                "content": "second answer",
+                "tool_calls": [], "invalid_tool_calls": [],
+                "additional_kwargs": {}, "response_metadata": {}, "name": None,
+                "usage_metadata": {"input_tokens": 0, "output_tokens": 0, "total_tokens": 0},
+            },
+        )
+
+        request = _make_request(event_store)
+        messages = await _get_event_store_messages(request, "t_sum")
+        assert messages is not None
+        # 4 messages, not 2 (which is what the summarized checkpoint would yield)
+        assert len(messages) == 4
+        assert messages[0]["content"][0]["text"] == "original question"
+        assert messages[1]["id"] == "lc_run--r1"
+        assert messages[3]["id"] == "lc_run--r2"
+
+    @pytest.mark.anyio
+    async def test_run_id_attached_to_every_message(self, event_store):
+        await _seed_simple_run(event_store, "t1", "r1")
+        request = _make_request(event_store)
+        messages = await _get_event_store_messages(request, "t1")
+        assert messages is not None
+        assert all(m.get("run_id") == "r1" for m in messages)
+
+    @pytest.mark.anyio
+    async def test_feedback_attached_only_to_final_ai_message_per_run(self, event_store):
+        await _seed_simple_run(event_store, "t1", "r1")
+        feedback_repo = _FakeFeedbackRepo(
+            {"r1": {"feedback_id": "fb1", "rating": 1, "comment": "great"}}
+        )
+        request = _make_request(event_store, feedback_repo=feedback_repo)
+        messages = await _get_event_store_messages(request, "t1")
+        assert messages is not None
+
+        # human (0), ai_tool_call (1), tool (2), ai_message (3)
+        final_ai = messages[3]
+        assert final_ai["feedback"] == {
+            "feedback_id": "fb1",
+            "rating": 1,
+            "comment": "great",
+        }
+        # Non-final messages must NOT have a feedback key at all — the
+        # frontend keys button visibility off of this.
+        assert "feedback" not in messages[0]
+        assert "feedback" not in messages[1]
+        assert "feedback" not in messages[2]
+
+    @pytest.mark.anyio
+    async def test_feedback_none_when_no_row_for_run(self, event_store):
+        await _seed_simple_run(event_store, "t1", "r1")
+        request = _make_request(event_store, feedback_repo=_FakeFeedbackRepo({}))
+        messages = await _get_event_store_messages(request, "t1")
+        assert messages is not None
+        # Final ai_message gets an explicit ``None`` — distinguishes "eligible
+        # but unrated" from "not eligible" (field absent).
+        assert messages[3]["feedback"] is None
+
+    @pytest.mark.anyio
+    async def test_feedback_per_run_for_multi_run_thread(self, event_store):
+        """A thread with two runs: each final ai_message should get its own feedback."""
+        # Run 1
+        await event_store.put(
+            thread_id="t_multi", run_id="r1",
+            event_type="human_message", category="message",
+            content={"type": "human", "id": None, "content": "q1",
+                     "additional_kwargs": {}, "response_metadata": {}, "name": None},
+        )
+        await event_store.put(
+            thread_id="t_multi", run_id="r1",
+            event_type="ai_message", category="message",
+            content={"type": "ai", "id": "lc_run--a1", "content": "a1",
+                     "tool_calls": [], "invalid_tool_calls": [],
+                     "additional_kwargs": {}, "response_metadata": {}, "name": None,
+                     "usage_metadata": None},
+        )
+        # Run 2
+        await event_store.put(
+            thread_id="t_multi", run_id="r2",
+            event_type="human_message", category="message",
+            content={"type": "human", "id": None, "content": "q2",
+                     "additional_kwargs": {}, "response_metadata": {}, "name": None},
+        )
+        await event_store.put(
+            thread_id="t_multi", run_id="r2",
+            event_type="ai_message", category="message",
+            content={"type": "ai", "id": "lc_run--a2", "content": "a2",
+                     "tool_calls": [], "invalid_tool_calls": [],
+                     "additional_kwargs": {}, "response_metadata": {}, "name": None,
+                     "usage_metadata": None},
+        )
+        feedback_repo = _FakeFeedbackRepo({
+            "r1": {"feedback_id": "fb_r1", "rating": 1, "comment": None},
+            "r2": {"feedback_id": "fb_r2", "rating": -1, "comment": "meh"},
+        })
+        request = _make_request(event_store, feedback_repo=feedback_repo)
+        messages = await _get_event_store_messages(request, "t_multi")
+        assert messages is not None
+        # human[r1], ai[r1], human[r2], ai[r2]
+        assert messages[1]["feedback"]["feedback_id"] == "fb_r1"
+        assert messages[1]["feedback"]["rating"] == 1
+        assert messages[3]["feedback"]["feedback_id"] == "fb_r2"
+        assert messages[3]["feedback"]["rating"] == -1
+        # Humans don't get feedback
+        assert "feedback" not in messages[0]
+        assert "feedback" not in messages[2]
+
+    @pytest.mark.anyio
+    async def test_feedback_repo_failure_does_not_break_helper(self, monkeypatch, event_store):
+        """If feedback lookup throws, messages still come back without feedback."""
+        await _seed_simple_run(event_store, "t1", "r1")
+
+        class _BoomRepo:
+            async def list_by_thread_grouped(self, *a, **kw):
+                raise RuntimeError("db down")
+
+        request = _make_request(event_store, feedback_repo=_BoomRepo())
+        messages = await _get_event_store_messages(request, "t1")
+        assert messages is not None
+        assert len(messages) == 4
+        for m in messages:
+            assert "feedback" not in m
+
+    @pytest.mark.anyio
+    async def test_returns_none_when_dep_raises(self, monkeypatch, event_store):
+        """When ``get_run_event_store`` is not configured, helper returns None."""
+        import app.gateway.routers.threads as threads_mod
+
+        def boom(_request):
+            raise RuntimeError("no store")
+
+        monkeypatch.setattr(threads_mod, "get_run_event_store", boom)
+        request = _make_request(event_store)
+        assert await threads_mod._get_event_store_messages(request, "t1") is None

backend/tests/test_threads_router.py

@@ -113,14 +113,8 @@ def test_delete_thread_data_returns_generic_500_error(tmp_path):
 # ── Server-reserved metadata key stripping ──────────────────────────────────
 
 
-def test_strip_reserved_metadata_removes_owner_id():
-    """Client-supplied owner_id is dropped to prevent reflection attacks."""
-    out = threads._strip_reserved_metadata({"owner_id": "victim-id", "title": "ok"})
-    assert out == {"title": "ok"}
-
-
 def test_strip_reserved_metadata_removes_user_id():
-    """user_id is also reserved (defense in depth for any future use)."""
+    """Client-supplied user_id is dropped to prevent reflection attacks."""
     out = threads._strip_reserved_metadata({"user_id": "victim-id", "title": "ok"})
     assert out == {"title": "ok"}
 
@@ -136,6 +130,6 @@ def test_strip_reserved_metadata_empty_input():
     assert threads._strip_reserved_metadata({}) == {}
 
 
-def test_strip_reserved_metadata_strips_both_simultaneously():
-    out = threads._strip_reserved_metadata({"owner_id": "x", "user_id": "y", "keep": "me"})
+def test_strip_reserved_metadata_strips_all_reserved_keys():
+    out = threads._strip_reserved_metadata({"user_id": "x", "keep": "me"})
     assert out == {"keep": "me"}

config.example.yaml

@@ -740,8 +740,8 @@ skill_evolution:
 # backend: sqlite  -- Single-node deployment, files in sqlite_dir
 # backend: postgres -- Production multi-node deployment
 #
-# SQLite mode automatically uses separate .db files for checkpointer
-# and application data to avoid write-lock contention.
+# SQLite mode uses a single deerflow.db file with WAL journal mode
+# for both checkpointer and application data.
 #
 # Postgres mode: put your connection URL in .env as DATABASE_URL,
 # then reference it here with $DATABASE_URL.

docs/superpowers/plans/2026-04-10-event-store-history.md

@@ -0,0 +1,471 @@
+# Event Store History — Backend Compatibility Layer
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Replace checkpoint state with the append-only event store as the message source in the thread state/history endpoints, so summarization never causes message loss.
+
+**Architecture:** The Gateway's `get_thread_state` and `get_thread_history` endpoints currently read messages from `checkpoint.channel_values["messages"]`. After summarization, those messages are replaced with a synthetic summary-as-human message and all pre-summarize messages are gone. We modify these endpoints to read messages from the RunEventStore instead (append-only, unaffected by summarization). The response shape for each message stays identical so the chat render path needs no changes, but the frontend's feedback hook must be aligned to use the same full-history view (see Task 4).
+
+**Tech Stack:** Python (FastAPI, SQLAlchemy), pytest, TypeScript (React Query)
+
+**Scope:** Gateway mode only (`make dev-pro`). Standard mode uses the LangGraph Server directly and does not go through these endpoints; the summarize bug is still present there and must be tracked as a separate follow-up (see §"Follow-ups" at end of plan).
+
+**Prerequisite already landed:** `backend/packages/harness/deerflow/runtime/journal.py` now unwraps `Command(update={'messages':[ToolMessage(...)]})` in `on_tool_end`, so new runs that use state-updating tools (e.g. `present_files`) write the inner `ToolMessage` content to the event store instead of `str(Command(...))`. Legacy data captured before this fix is cleaned up defensively by the new helper (see Task 1 Step 3 `_sanitize_legacy_command_repr`).
+
+---
+
+## Real Data Alignment Analysis
+
+Compared real `POST /history` response (checkpoint-based) with `run_events` table for thread `6d30913e-dcd4-41c8-8941-f66c716cf359` (docs/resp.json + backend/.deer-flow/data/deerflow.db). See `docs/superpowers/specs/2026-04-11-runjournal-history-evaluation.md` for full evidence chain.
+
+| Message type | Fields compared | Difference |
+|-------------|----------------|------------|
+| human_message | all fields | `id` is `None` in event store, has UUID in checkpoint |
+| ai_message (tool_call) | all fields, 6 overlapping | **IDENTICAL** (0 diffs) |
+| ai_message (final) | all fields | **IDENTICAL** |
+| tool_result (normal) | all fields | Only `id` differs (`None` vs UUID) |
+| tool_result (from `Command`-returning tool) | content | **Legacy data stored `str(Command(...))` repr instead of inner ToolMessage** — fixed in journal.py for new runs; legacy rows sanitized by helper |
+
+**Root cause for id difference:** LangGraph's checkpoint assigns `id` to HumanMessage and ToolMessage during graph execution. Event store writes happen earlier, when those ids are still None. AI messages receive `id` from the LLM response (`lc_run--*`) and are unaffected.
+
+**Fix for id:** Generate deterministic UUIDs for `id=None` messages using `uuid5(NAMESPACE_URL, f"{thread_id}:{seq}")` at read time. Patch a **copy** of the content dict, never the live store object.
+
+**Summarize impact quantified on the reproducer thread**: event_store has 16 messages (7 AI + 9 others); checkpoint has 12 after summarize (5 AI + 7 others). AI id overlap: 5 of 7 — the 2 missing AI messages are pre-summarize.
+
+---
+
+## File Structure
+
+| File | Action | Responsibility |
+|------|--------|----------------|
+| `backend/app/gateway/routers/threads.py` | Modify | Replace checkpoint messages with event store messages in `get_thread_state` and `get_thread_history` |
+| `backend/tests/test_thread_state_event_store.py` | Create | Tests for the modified endpoints |
+
+---
+
+### Task 1: Add `_get_event_store_messages` helper to `threads.py`
+
+A shared helper that loads the **full** message stream from the event store, patches `id=None` messages with deterministic UUIDs, and defensively sanitizes legacy `Command(update=...)` reprs captured before the journal.py fix. Patches a copy of each content dict so the live store is never mutated.
+
+**Design constraints (derived from evaluation §3, §4, §5):**
+- **Full pagination**, not `limit=1000`. `RunEventStore.list_messages` returns "latest N records" — a fixed limit silently truncates older messages. Use `count_messages()` to size the request or loop with `after_seq` cursors.
+- **Copy before mutate**. `MemoryRunEventStore` returns live dict references; the JSONL/DB stores may return detached rows but we must not rely on that. Always `content = dict(evt["content"])` before patching `id`.
+- **Legacy Command sanitization.** Legacy data contains `content["content"] == "Command(update={'artifacts': [...], 'messages': [ToolMessage(content='X', ...)]})"`. Regex-extract the inner ToolMessage content string and replace; if extraction fails, leave content as-is (still strictly better than nothing because checkpoint fallback is also wrong for summarized threads).
+- **User context.** `DbRunEventStore.list_messages` is user-scoped via `resolve_user_id(AUTO)` and relies on the auth contextvar set by `@require_permission`. Both endpoints are already decorated — document this dependency in the helper docstring.
+
+**Files:**
+- Modify: `backend/app/gateway/routers/threads.py`
+- Test: `backend/tests/test_thread_state_event_store.py`
+
+- [ ] **Step 1: Write the test**
+
+Create `backend/tests/test_thread_state_event_store.py`:
+
+```python
+"""Tests for event-store-backed message loading in thread state/history endpoints."""
+
+from __future__ import annotations
+
+import uuid
+
+import pytest
+
+from deerflow.runtime.events.store.memory import MemoryRunEventStore
+
+
+@pytest.fixture()
+def event_store():
+    return MemoryRunEventStore()
+
+
+async def _seed_conversation(event_store: MemoryRunEventStore, thread_id: str = "t1"):
+    """Seed a realistic multi-turn conversation matching real checkpoint format."""
+    # human_message: id is None (same as real data)
+    await event_store.put(
+        thread_id=thread_id, run_id="r1",
+        event_type="human_message", category="message",
+        content={
+            "type": "human", "id": None,
+            "content": [{"type": "text", "text": "Hello"}],
+            "additional_kwargs": {}, "response_metadata": {}, "name": None,
+        },
+    )
+    # ai_tool_call: id is set by LLM
+    await event_store.put(
+        thread_id=thread_id, run_id="r1",
+        event_type="ai_tool_call", category="message",
+        content={
+            "type": "ai", "id": "lc_run--abc123",
+            "content": "",
+            "tool_calls": [{"name": "search", "args": {"q": "cats"}, "id": "call_1", "type": "tool_call"}],
+            "invalid_tool_calls": [],
+            "additional_kwargs": {}, "response_metadata": {}, "name": None,
+            "usage_metadata": {"input_tokens": 100, "output_tokens": 50, "total_tokens": 150},
+        },
+    )
+    # tool_result: id is None (same as real data)
+    await event_store.put(
+        thread_id=thread_id, run_id="r1",
+        event_type="tool_result", category="message",
+        content={
+            "type": "tool", "id": None,
+            "content": "Found 10 results",
+            "tool_call_id": "call_1", "name": "search",
+            "artifact": None, "status": "success",
+            "additional_kwargs": {}, "response_metadata": {},
+        },
+    )
+    # ai_message: id is set by LLM
+    await event_store.put(
+        thread_id=thread_id, run_id="r1",
+        event_type="ai_message", category="message",
+        content={
+            "type": "ai", "id": "lc_run--def456",
+            "content": "I found 10 results about cats.",
+            "tool_calls": [], "invalid_tool_calls": [],
+            "additional_kwargs": {}, "response_metadata": {"finish_reason": "stop"}, "name": None,
+            "usage_metadata": {"input_tokens": 200, "output_tokens": 100, "total_tokens": 300},
+        },
+    )
+    # Also add a trace event — should NOT appear
+    await event_store.put(
+        thread_id=thread_id, run_id="r1",
+        event_type="llm_request", category="trace",
+        content={"model": "gpt-4"},
+    )
+
+
+class TestGetEventStoreMessages:
+    """Verify event store message extraction with id patching."""
+
+    @pytest.mark.asyncio
+    async def test_extracts_all_message_types(self, event_store):
+        await _seed_conversation(event_store)
+        events = await event_store.list_messages("t1", limit=500)
+        messages = [evt["content"] for evt in events if isinstance(evt.get("content"), dict) and "type" in evt["content"]]
+        assert len(messages) == 4
+        assert [m["type"] for m in messages] == ["human", "ai", "tool", "ai"]
+
+    @pytest.mark.asyncio
+    async def test_null_ids_get_patched(self, event_store):
+        """Messages with id=None should get deterministic UUIDs."""
+        await _seed_conversation(event_store)
+        events = await event_store.list_messages("t1", limit=500)
+        messages = []
+        for evt in events:
+            content = evt.get("content")
+            if isinstance(content, dict) and "type" in content:
+                if content.get("id") is None:
+                    content["id"] = str(uuid.uuid5(uuid.NAMESPACE_URL, f"t1:{evt['seq']}"))
+                messages.append(content)
+
+        # All messages now have an id
+        for m in messages:
+            assert m["id"] is not None
+            assert isinstance(m["id"], str)
+            assert len(m["id"]) > 0
+
+        # AI messages keep their original id
+        assert messages[1]["id"] == "lc_run--abc123"
+        assert messages[3]["id"] == "lc_run--def456"
+
+        # Human and tool messages get deterministic ids (same input = same output)
+        human_id_1 = str(uuid.uuid5(uuid.NAMESPACE_URL, "t1:1"))
+        assert messages[0]["id"] == human_id_1
+
+    @pytest.mark.asyncio
+    async def test_empty_thread(self, event_store):
+        events = await event_store.list_messages("nonexistent", limit=500)
+        messages = [evt["content"] for evt in events if isinstance(evt.get("content"), dict)]
+        assert messages == []
+
+    @pytest.mark.asyncio
+    async def test_tool_call_fields_preserved(self, event_store):
+        await _seed_conversation(event_store)
+        events = await event_store.list_messages("t1", limit=500)
+        messages = [evt["content"] for evt in events if isinstance(evt.get("content"), dict) and "type" in evt["content"]]
+
+        # AI tool_call message
+        ai_tc = messages[1]
+        assert ai_tc["tool_calls"][0]["name"] == "search"
+        assert ai_tc["tool_calls"][0]["id"] == "call_1"
+
+        # Tool result
+        tool = messages[2]
+        assert tool["tool_call_id"] == "call_1"
+        assert tool["status"] == "success"
+```
+
+- [ ] **Step 2: Run tests to verify they pass**
+
+Run: `cd backend && PYTHONPATH=. uv run pytest tests/test_thread_state_event_store.py -v`
+
+- [ ] **Step 3: Add the helper function and modify `get_thread_history`**
+
+In `backend/app/gateway/routers/threads.py`:
+
+1. Add import at the top:
+```python
+import uuid  # ADD (may already exist, check first)
+from app.gateway.deps import get_run_event_store  # ADD
+```
+
+2. Add the helper function (before the endpoint functions, after the model definitions):
+
+```python
+_LEGACY_CMD_INNER_CONTENT_RE = re.compile(
+    r"ToolMessage\(content=(?P<q>['\"])(?P<inner>.*?)(?P=q)",
+    re.DOTALL,
+)
+
+
+def _sanitize_legacy_command_repr(content_field: Any) -> Any:
+    """Recover the inner ToolMessage text from a legacy ``str(Command(...))`` repr.
+
+    Runs that pre-date the ``on_tool_end`` fix in ``journal.py`` stored
+    ``str(Command(update={'messages':[ToolMessage(content='X', ...)]}))`` as the
+    tool_result content. New runs store ``'X'`` directly. For old threads, try
+    to extract ``'X'`` defensively; return the original string if extraction
+    fails (still no worse than the current checkpoint-based fallback, which is
+    broken for summarized threads anyway).
+    """
+    if not isinstance(content_field, str) or not content_field.startswith("Command(update="):
+        return content_field
+    match = _LEGACY_CMD_INNER_CONTENT_RE.search(content_field)
+    return match.group("inner") if match else content_field
+
+
+async def _get_event_store_messages(request: Request, thread_id: str) -> list[dict] | None:
+    """Load messages from the event store, returning None if unavailable.
+
+    The event store is append-only and immune to summarization. Each
+    message event's ``content`` field contains a ``model_dump()``'d
+    LangChain Message dict that is already JSON-serialisable.
+
+    **Full pagination, not a fixed limit.** ``RunEventStore.list_messages``
+    returns the newest ``limit`` records when no cursor is given, which
+    silently drops older messages. We call ``count_messages()`` first and
+    request that many records. For stores that may return fewer (e.g. filtered
+    by user), we also fall back to ``after_seq``-cursor pagination.
+
+    **Copy-on-read.** Each content dict is copied before ``id`` is patched so
+    the live store object is never mutated; ``MemoryRunEventStore`` returns
+    live references.
+
+    **Legacy Command repr sanitization.** See ``_sanitize_legacy_command_repr``.
+
+    **User context.** ``DbRunEventStore`` is user-scoped by default via
+    ``resolve_user_id(AUTO)`` (see ``runtime/user_context.py``). Callers of
+    this helper must be inside a request where ``@require_permission`` has
+    populated the user contextvar. Both ``get_thread_history`` and
+    ``get_thread_state`` satisfy that. Do not call this helper from CLI or
+    migration scripts without passing ``user_id=None`` explicitly.
+
+    Returns ``None`` when the event store is not configured or contains no
+    messages for this thread, so callers can fall back to checkpoint messages.
+    """
+    try:
+        event_store = get_run_event_store(request)
+    except Exception:
+        return None
+
+    try:
+        total = await event_store.count_messages(thread_id)
+    except Exception:
+        logger.exception("count_messages failed for thread %s", sanitize_log_param(thread_id))
+        return None
+    if not total:
+        return None
+
+    # Batch by page_size to keep memory bounded for very long threads.
+    page_size = 500
+    collected: list[dict] = []
+    after_seq: int | None = None
+    while True:
+        page = await event_store.list_messages(thread_id, limit=page_size, after_seq=after_seq)
+        if not page:
+            break
+        collected.extend(page)
+        if len(page) < page_size:
+            break
+        after_seq = page[-1].get("seq")
+        if after_seq is None:
+            break
+
+    messages: list[dict] = []
+    for evt in collected:
+        raw = evt.get("content")
+        if not isinstance(raw, dict) or "type" not in raw:
+            continue
+        # Copy to avoid mutating the store-owned dict.
+        content = dict(raw)
+        if content.get("id") is None:
+            content["id"] = str(uuid.uuid5(uuid.NAMESPACE_URL, f"{thread_id}:{evt['seq']}"))
+        # Sanitize legacy Command reprs on tool_result messages only.
+        if content.get("type") == "tool":
+            content["content"] = _sanitize_legacy_command_repr(content.get("content"))
+        messages.append(content)
+    return messages if messages else None
+```
+
+Also add `import re` at the top of the file if it isn't already imported.
+
+3. In `get_thread_history` (around line 585-590), replace the messages section:
+
+**Before:**
+```python
+            # Attach messages from checkpointer only for the latest checkpoint
+            if is_latest_checkpoint:
+                messages = channel_values.get("messages")
+                if messages:
+                    values["messages"] = serialize_channel_values({"messages": messages}).get("messages", [])
+            is_latest_checkpoint = False
+```
+
+**After:**
+```python
+            # Attach messages: prefer event store (immune to summarization),
+            # fall back to checkpoint messages when event store is unavailable.
+            if is_latest_checkpoint:
+                es_messages = await _get_event_store_messages(request, thread_id)
+                if es_messages is not None:
+                    values["messages"] = es_messages
+                else:
+                    messages = channel_values.get("messages")
+                    if messages:
+                        values["messages"] = serialize_channel_values({"messages": messages}).get("messages", [])
+            is_latest_checkpoint = False
+```
+
+- [ ] **Step 4: Modify `get_thread_state` similarly**
+
+In `get_thread_state` (around line 443-444), replace:
+
+**Before:**
+```python
+    return ThreadStateResponse(
+        values=serialize_channel_values(channel_values),
+```
+
+**After:**
+```python
+    values = serialize_channel_values(channel_values)
+
+    # Override messages with event store data (immune to summarization)
+    es_messages = await _get_event_store_messages(request, thread_id)
+    if es_messages is not None:
+        values["messages"] = es_messages
+
+    return ThreadStateResponse(
+        values=values,
+```
+
+- [ ] **Step 5: Run all backend tests**
+
+Run: `cd backend && PYTHONPATH=. uv run pytest tests/ -v --timeout=30 -x`
+
+- [ ] **Step 6: Commit**
+
+```bash
+git add backend/app/gateway/routers/threads.py backend/tests/test_thread_state_event_store.py
+git commit -m "feat(threads): load messages from event store instead of checkpoint state
+
+Event store is append-only and immune to summarization. Messages with
+null ids (human, tool) get deterministic UUIDs based on thread_id:seq
+for stable frontend rendering."
+```
+
+---
+
+### Task 2 (OPTIONAL, deferred): Reduce flush_threshold for shorter mid-stream gap
+
+**Status:** Not a correctness fix. Re-evaluation (see spec) found that `RunJournal` already flushes on `run_end`, `run_error`, cancel, and worker `finally` paths. The only window this tuning narrows is a hard process crash or mid-run reload. Defer and decide separately; do not couple with Task 1 merge.
+
+If pursued: change `flush_threshold` default from 20 → 5 in `journal.py:42`, rerun `tests/test_run_journal.py`, commit as a separate `perf(journal): …` commit.
+
+---
+
+### Task 3: Fix `useThreadFeedback` pagination in frontend
+
+Once `/history` returns the full event-store-backed message stream, the frontend's `runIdByAiIndex` map must also cover the full stream or its positional AI-index mapping drifts and feedback clicks go to the wrong `run_id`. The current hook hardcodes `limit=200`.
+
+**Files:**
+- Modify: `frontend/src/core/threads/hooks.ts` (around line 679)
+
+- [ ] **Step 1: Replace the fixed `?limit=200` with full pagination**
+
+Change:
+
+```ts
+const res = await fetchWithAuth(
+  `${getBackendBaseURL()}/api/threads/${encodeURIComponent(threadId)}/messages?limit=200`,
+);
+```
+
+to a loop that pages via `after_seq` (or an equivalent query param exposed by the `/messages` endpoint — check `backend/app/gateway/routers/thread_runs.py:285-323` for the actual parameter names before writing the TS code). Accumulate `messages` until a page returns fewer than the page size.
+
+- [ ] **Step 2: Defensive index guard**
+
+`runIdByAiIndex[aiMessageIndex]` can still be `undefined` when the frontend renders optimistic state before the messages query refreshes. The current `?? undefined` in `message-list.tsx:71` already handles this; do not remove it.
+
+- [ ] **Step 3: Invalidate `["thread-feedback", threadId]` after a new run**
+
+In `useThreadStream` (or wherever stream-end is handled), call `queryClient.invalidateQueries({ queryKey: ["thread-feedback", threadId] })` when the stream closes so the runIdByAiIndex picks up the new run's AI message immediately.
+
+- [ ] **Step 4: Run `pnpm check`**
+
+```bash
+cd frontend && pnpm check
+```
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add frontend/src/core/threads/hooks.ts
+git commit -m "fix(feedback): paginate useThreadFeedback and invalidate after stream"
+```
+
+---
+
+### Task 4: End-to-end test — summarize + multi-run feedback
+
+Add a regression test that exercises the exact bug class we are fixing: a summarized thread with at least two runs, where feedback clicks must target the correct `run_id`.
+
+**Files:**
+- Modify: `backend/tests/test_thread_state_event_store.py`
+
+- [ ] **Step 1: Write the test**
+
+Seed a `MemoryRunEventStore` with two runs worth of messages (`r1`: human + ai + human + ai, `r2`: human + ai), then simulate a summarized checkpoint state that drops the `r1` messages. Call `_get_event_store_messages` and assert:
+
+- Length matches the event store, not the checkpoint
+- The first message is the original `r1` human, not a summary
+- AI messages preserve their `lc_run--*` ids in order
+- Any `id=None` messages get a stable `uuid5(...)` id
+- A legacy `str(Command(update=...))` content field in a tool_result is sanitized to the inner text
+
+- [ ] **Step 2: Run the new test**
+
+```bash
+cd backend && PYTHONPATH=. uv run pytest tests/test_thread_state_event_store.py -v
+```
+
+- [ ] **Step 3: Commit with Tasks 1, 3 changes**
+
+Bundle with the Task 1 commit so tests always land alongside the implementation.
+
+---
+
+### Task 5: Standard mode follow-up (documentation only)
+
+Standard mode (`make dev`) hits LangGraph Server directly for `/threads/{id}/history` and does not go through the Gateway router we just patched. The summarize bug is still present there.
+
+**Files:**
+- Modify: this plan (add follow-up section at the bottom, see below) OR create a separate tracking issue
+
+- [ ] **Step 1: Record the gap**
+
+Append to the bottom of this plan (or open a GitHub issue and link it):
+
+> **Follow-up — Standard mode summarize bug**
+> `get_thread_history` in `backend/app/gateway/routers/threads.py` is only hit in Gateway mode. Standard mode proxies `/api/langgraph/*` directly to the LangGraph Server (see `backend/CLAUDE.md` nginx routing and `frontend/CLAUDE.md` `NEXT_PUBLIC_LANGGRAPH_BASE_URL`). The summarize-message-loss symptom is still reproducible there. Options: (a) teach the LangGraph Server checkpointer to branch on an override, (b) move `/history` behind Gateway in Standard mode as well, (c) accept as known limitation for Standard mode. Decide before GA.

docs/superpowers/specs/2026-04-11-runjournal-history-evaluation.md

@@ -0,0 +1,191 @@
+# RunJournal 替换 History Messages — 方案评估与对比
+
+**日期**：2026-04-11
+**分支**：`rayhpeng/fix-persistence-new`
+**相关 plan**：[`docs/superpowers/plans/2026-04-10-event-store-history.md`](../plans/2026-04-10-event-store-history.md)（尚未落地）
+
+---
+
+## 1. 问题与数据核对
+
+**症状**：SummarizationMiddleware 触发后，前端历史中无法展示 summarize 之前的真实用户消息。
+
+**复现数据**（thread `6d30913e-dcd4-41c8-8941-f66c716cf359`）：
+
+| 数据源 | seq=1 的 message | 总 message 数 | 是否保留原始 human |
+|---|---|---:|---|
+| `run_events`（SQLite） | human `"最新伊美局势"` | 9（1 human + 7 ai_tool_call + 9 tool_result + 1 ai_message） | ✅ |
+| `/history` 响应（`docs/resp.json`） | type=human，content=`"Here is a summary of the conversation to date:…"` | 不定 | ❌（已被 summary 替换）|
+
+**根因**：`backend/app/gateway/routers/threads.py:587-589` 的 `get_thread_history` 从 `checkpoint.channel_values["messages"]` 读取，而 LangGraph 的 SummarizationMiddleware 会原地改写这个列表。
+
+---
+
+## 2. 候选方案
+
+| 方案 | 描述 | 本次是否推荐 |
+|---|---|---|
+| **A. event_store 覆盖 messages**（已有 plan） | `/history`、`/state` 改读 `RunEventStore.list_messages()`，覆盖 `channel_values["messages"]`；其它字段保持 checkpoint 来源 | ✅ 主方案 |
+| B. 修 SummarizationMiddleware | 让 summarize 不原地替换 messages（作为附加 system message） | ❌ 违背 summarize 的 token 预算初衷 |
+| C. 双读合并（checkpoint + event_store diff） | 合并 summarize 切点前后的两段 | ❌ 合并逻辑复杂无额外收益 |
+| D. 切到现有 `/api/threads/{id}/messages` 端点 | 前端直接消费已经存在的 event-store 消息端点（`thread_runs.py:285-323`）| ⚠️ 更干净但需要前端改动 |
+
+---
+
+## 3. Claude 自评 vs Codex 独立评估
+
+两方独立分析了同一份 plan。重合点基本一致，但 **Codex 发现了一个我遗漏的关键 bug**。
+
+### 3.1 一致结论
+
+| 维度 | 结论 |
+|---|---|
+| 正确性方向 | event_store 是 append-only + 不受 summarize 影响，方向正确 |
+| ID 补齐 | `uuid5(NAMESPACE_URL, f"{thread_id}:{seq}")` 稳定且确定性，安全 |
+| 前端 schema | 零改动 |
+| Non-message 字段（artifacts/todos/title/thread_data） | summarize 只影响 messages，不需要覆盖其它字段 |
+| 多 checkpoint 语义 | 前端 `useStream` 只取 `limit: 1`（`frontend/src/core/threads/hooks.ts:203-210`），不做时间旅行；latest-only 可接受但应在注释/文档写清楚 |
+| 作用域 | 仅 Gateway mode；Standard mode 直连 LangGraph Server，bug 在默认部署路径仍然存在 |
+
+### 3.2 Claude 的独立观察
+
+1. 已验证数据对齐：plan 文档第 15-28 行的真实数据对齐表与本次 `run_events` 导出一致（9 条消息 id 分布：AI 来自 LLM `lc_run--*`、human/tool 为 None）。
+2. 担心 `run_end` / `run_error` / `cancel` 路径未必都 flush —— 这一点 Codex 实际核查了代码并给出确定结论（见下）。
+3. 方案 A 的单文件改动约 60 行，复杂度小。
+
+### 3.3 Codex 的关键补充（Claude 遗漏）
+
+> **Bug #1 — Plan 用 `limit=1000` 并非全量**
+> `RunEventStore.list_messages()` 的语义是"返回最新 limit 条"（`base.py:51-65`、`db.py:151-181`）。对于消息数超过 1000 的长对话，plan 当前写法会**丢掉最早的消息**，再次引入"消息丢失"bug（只是换了丢失的段）。
+
+> **Bug #2 — helper 就地修改了 store 的 dict**
+> plan 的 helper 里对 `content` 原地写 `id`；`MemoryRunEventStore` 返回的是**活引用**，会污染 store 中的对象。应 deep-copy 或 dict 推导出新对象。
+
+> **Flush 路径已核查**：
+> `RunJournal` 在 threshold (`journal.py:360-373`)、`run_end` (`91-96`)、`run_error` (`97-106`)、worker `finally` (`worker.py:280-286`) 都会 flush；`CancelledError` 也走 finally。**正常 end/error/cancel 都 flush，仅硬 kill / 进程崩溃会丢缓冲区**。
+> 因此 `flush_threshold 20 → 5` 的意义**仅在于硬崩溃窗口**与 mid-run reload 可见性，**不是正确性修复**，属于可选 tuning。代价是更多 put_batch / SQLite churn；且 `_flush_sync()` (`383-398`) 已防止并发 flush，所以"每 5 条一 flush"是 best-effort 非严格保证。
+
+### 3.4 Codex 未否决但提示的次要点
+
+- 方案 D（消费现有 `/api/threads/{id}/messages` 端点）更干净但需前端改动。
+- `/history` 一旦被方案 A 改过，就不再是严格意义上的"按 checkpoint 快照"API（对 messages 字段），应写进注释和 API 文档。
+- Standard mode 的 summarize bug 应建立独立 follow-up issue。
+
+---
+
+## 4. 最终合并判决
+
+**Codex**：APPROVE-WITH-CHANGES
+**Claude**：同意 Codex 的判决
+
+### 合并前必须修改（Top 3）
+
+1. **修复分页 bug**：不能用固定 `limit=1000`。必须用以下之一：
+   - `count = await event_store.count_messages(thread_id)`，再 `list_messages(thread_id, limit=count)`
+   - 或循环 cursor 分页（`after_seq`）直到耗尽
+2. **不要原地修改 store dict**：helper 对 `content` 的 id 补齐需要 copy（`dict(content)` 浅拷贝足够，因为只写 top-level `id`）
+3. **Standard mode 显式 follow-up**：在 plan 文末加 "Standard-mode follow-up: TODO #xxx"，或在合并 PR 描述中明确这是 Gateway-only 止血
+
+### 可选（非阻塞）
+
+4. `flush_threshold 20 → 5` 降级为"可选 tuning"，不是修复的一部分；或独立一条 commit 并说明只对硬崩溃窗口有用
+5. `get_thread_history` 新增注释，说明 messages 字段脱离了 checkpoint 快照语义
+6. 测试覆盖：模拟 summarize 后的 checkpoint + 真实 event_store，端到端验证 `/history` 返回包含原始 human 消息
+
+---
+
+## 5. 推荐执行顺序
+
+1. 按本文档 §4 修订 `docs/superpowers/plans/2026-04-10-event-store-history.md`（主要是 Task 1 的 helper 实现 + 分页）
+2. 按修订后的 plan 执行（走 `superpowers:executing-plans`）
+3. 合并后立即建 Standard mode follow-up issue
+
+## 6. Feedback 影响分析（2026-04-11 补充）
+
+### 6.1 数据模型
+
+`feedback` 表（`persistence/feedback/model.py`）：
+
+| 字段 | 说明 |
+|---|---|
+| `feedback_id` PK | - |
+| `run_id` NOT NULL | 反馈目标 run |
+| `thread_id` NOT NULL | - |
+| `user_id` | - |
+| `message_id` nullable | 注释明确写：`optional RunEventStore event identifier` — 已经面向 event_store 设计 |
+| UNIQUE(thread_id, run_id, user_id) | 每 run 每用户至多一条 |
+
+**结论**：feedback **不按 message uuid 存**，按 `run_id` 存，所以 summarize 导致的 checkpoint messages 丢失**不会影响 feedback 存储**。schema 天生与 event_store 兼容，**无需数据迁移**。
+
+### 6.2 前端的 runId 映射：发现隐藏 bug
+
+前端 feedback 目前走两条并行的数据链：
+
+| 用途 | 数据源 | 位置 |
+|---|---|---|
+| 渲染消息体 | `POST /history`（checkpoint） | `useStream` → `thread.messages` |
+| 拿 `runId` 映射 | `GET /api/threads/{id}/messages?limit=200`（**event_store**） | `useThreadFeedback` (`hooks.ts:669-709`) |
+
+两者通过 **"AI 消息的序号"** 对齐：
+
+```ts
+// hooks.ts:691-698
+for (const msg of messages) {
+  if (msg.event_type === "ai_message") {
+    runIdByAiIndex.push(msg.run_id);  // 只按 AI 顺序 push
+  }
+}
+// message-list.tsx:70-71
+runId = feedbackData.runIdByAiIndex[aiMessageIndex]
+```
+
+**Bug**：summarize 过的 thread 里，两条数据链的 AI 消息数量和顺序**不一致**：
+
+| 数据源 | 本 thread 的 AI 消息序列 | 数量 |
+|---|---|---:|
+| `/history`（checkpoint，summarize 后） | seq=19,31,37,45,53 | 5 |
+| `/messages`（event_store，完整） | seq=5,13,19,31,37,45,53 | 7 |
+
+结果：前端渲染的"第 0 条 AI 消息"是 seq=19，但 `runIdByAiIndex[0]` 指向 seq=5 的 run（本例同一 run 里没事，**跨多 run 的 thread 点赞就会打到错的 run 上**）。
+
+**这个 bug 和本次 plan 无关，已经存在了**。只是用户未必注意到。
+
+### 6.3 方案 A 对 feedback 的影响
+
+**负面**：无。feedback 存储不受影响。
+
+**正面（意外收益）**：`/history` 切换到 event_store 后，**两条数据链的 AI 消息序列自动对齐**，§6.2 的隐藏 bug 被顺带修好。
+
+**前提条件**（加入 Top 3 改动之一同等重要）：
+
+- 新 helper 必须和 `/messages` 端点用**同样的消息获取逻辑**（same store, same filter）。否则两条链仍然可能在边界条件下漂移
+- 具体说：**两边都要做完整分页**。目前 `/messages?limit=200` 在前端硬编码 200，如果 thread 有 >200 条消息就会截断；plan 的 `limit=1000` 也一样有上限。两个上限不一致 → 两边顺序不再对齐 → feedback 映射错位
+- **必须修**：`useThreadFeedback` 的 `limit=200` 需要改成分页获取全部，或者 `/messages` 后端改为默认全量
+
+### 6.4 对前端改造顺序的影响
+
+原 plan 声明"零前端改动"，但加入 feedback 考虑后应修正为：
+
+| 改动 | 必须 | 可选 |
+|---|---|---|
+| 后端 `/history` 改读 event_store | ✅ | - |
+| 后端 helper 用分页而非 `limit=1000` | ✅ | - |
+| 前端 `useThreadFeedback` 改用分页或提升 limit | ✅ | - |
+| `runIdByAiIndex` 增加防御：索引越界 fallback `undefined`（已有）| - | ✅ 已经是 |
+| 前端改用 `/messages` 直接做渲染（方案 D） | - | ✅ 长期更干净 |
+
+### 6.5 feedback 相关的新 Top 3 补充
+
+在原来的 Top 3 之外，再加：
+
+4. **前端 `useThreadFeedback` 必须分页或拉全**（`frontend/src/core/threads/hooks.ts:679`），否则和 `/history` 的新全量行为仍然错位
+5. **端到端测试**：一个 thread 跨 >1 个 run + 触发 summarize + 给历史 AI 消息点赞，确认 feedback 打到正确的 run_id
+6. **TanStack Query 缓存协调**：`thread-feedback` 与 history 查询的 `staleTime` / invalidation 需要在新 run 结束时同步刷新，否则新消息写入后 `runIdByAiIndex` 没更新，点赞会打到上一个 run
+
+---
+
+## 8. 未决问题
+
+- `RunEventStore.count_messages()` 与 `list_messages(after_seq=...)` 的实际性能（SQLite 上对于数千消息级别应无问题，但未压测）
+- `MemoryRunEventStore` 与 `DbRunEventStore` 分页语义是否一致（Codex 只核查了 `db.py`，`memory.py` 需确认）
+- 是否应把 `/api/threads/{id}/messages` 提升为前端主用 endpoint，把 `/history` 保留为纯 checkpoint API —— 架构层面更干净但成本更高

docs/superpowers/specs/2026-04-11-summarize-marker-design.md

@@ -0,0 +1,203 @@
+# Summarize Marker in History — Design & Verification
+
+**Date**: 2026-04-11
+**Branch**: `rayhpeng/fix-persistence-new`
+**Status**: Design approved, implementation deferred to a follow-up PR
+**Depends on**: [`2026-04-11-runjournal-history-evaluation.md`](./2026-04-11-runjournal-history-evaluation.md) (the event-store-backed history fix this builds on)
+
+---
+
+## 1. Goal
+
+Display a "summarization happened here" marker in the conversation history UI when `SummarizationMiddleware` ran mid-run, so users understand why earlier messages look condensed or missing. The event-store-backed `/history` fix already recovered the original messages; this spec adds a **visible marker** at the seq position where summarization occurred, optionally showing the generated summary text.
+
+## 2. Investigation findings
+
+### 2.1 Today's state: zero middleware records
+
+Full scan of `backend/.deer-flow/data/deerflow.db` `run_events`:
+
+| category | rows |
+|---|---:|
+| trace | 76 |
+| message | 34 |
+| lifecycle | 8 |
+| **middleware** | **0** |
+
+No row has `event_type` containing `summariz` or `middleware`. The middleware category is dead in production.
+
+### 2.2 Why: two dead code paths in `journal.py`
+
+| Location | Status |
+|---|---|
+| `journal.py:343-362` — `on_custom_event("summarization", ...)` writes one trace event + one `category="middleware"` event. | Dead. Only fires when something calls `adispatch_custom_event("summarization", {...})`. The upstream LangChain `SummarizationMiddleware` (`.venv/.../langchain/agents/middleware/summarization.py:272`) **never emits custom events** — its `before_model`/`abefore_model` just mutate messages in place and return `{'messages': new_messages}`. Callback never triggered. |
+| `journal.py:449` — `record_middleware(tag, *, name, hook, action, changes)` helper | Dead. Grep shows zero callers in the harness. Added speculatively, never wired up. |
+
+### 2.3 Concrete evidence of summarize running unlogged
+
+Thread `3d5dea4a-0983-4727-a4e8-41a64428933a`:
+
+- `run_events` seq=1 → original human `"写一份关于deer-flow的详细技术报告"` ✓ (event store is fine)
+- `run_events` seq=43 → `llm_request` trace whose `messages[0]` literal contains `"Here is a summary of the conversation to date:"` — proof that SummarizationMiddleware did inject a summary mid-run
+- Zero rows with `category='middleware'` for this thread → nothing captured for UI to render
+
+## 3. Approaches considered
+
+### A. Subclass `SummarizationMiddleware` and dispatch a custom event
+
+Wrap the upstream class, override `abefore_model`, call `await adispatch_custom_event("summarization", {...})` after super(). Journal's existing `on_custom_event` path captures it.
+
+### B. Frontend-only diff heuristic
+
+Compare `event_store.count_messages()` vs rendered count, infer summarization happened from the gap. **Rejected**: can't pinpoint position in the stream, can't show summary text. Only yields a vague badge.
+
+### C. Hybrid A + frontend inline card rendered at the middleware event's seq position
+
+Same backend as A, plus frontend renders an inline `[N messages condensed]` card at the correct chronological position. **Recommended terminal state**.
+
+## 4. Subagent's wrong claim and its rebuttal
+
+An independent agent flagged approach A as structurally broken because:
+
+> `RunnableCallable(trace=False)` skips `set_config_context`, therefore `var_child_runnable_config` is never set, therefore `adispatch_custom_event` raises `RuntimeError("Unable to dispatch an adhoc event without a parent run id")`.
+
+**This is wrong.** The user's counter-intuition was correct: `trace=False` does not prevent `adispatch_custom_event` from working, as long as the middleware signature explicitly accepts `config: RunnableConfig`. The mechanism:
+
+1. `RunnableCallable.__init__` (`langgraph/_internal/_runnable.py:293-319`) inspects the function signature. If it accepts `config: RunnableConfig`, that parameter is recorded in `self.func_accepts`.
+2. Both `trace=True` and `trace=False` branches of `ainvoke` run the same kwarg-injection loop (`_runnable.py:349-356`): `if kw == "config": kw_value = config`. The `config` passed to `ainvoke` (from Pregel's `task.proc.ainvoke(task.input, config)` at `pregel/_retry.py:138`) is the task config with callbacks already bound.
+3. Inside the middleware, passing that `config` explicitly to `adispatch_custom_event(..., config=config)` means the function doesn't rely on `var_child_runnable_config.get()` at all. The LangChain docstring at `langchain_core/callbacks/manager.py:2574-2579` even says "If using python 3.10 and async, you MUST specify the config parameter" — which is exactly this path.
+
+`trace=False` only changes whether **this runnable layer creates a new child callback scope**. It does not affect whether the outer-layer config (with callbacks including `RunJournal`) is passed down to the function.
+
+## 5. Verification
+
+Ran `/tmp/verify_summarize_event.py` (standalone minimal reproduction):
+
+- Minimal `AgentMiddleware` subclass with `abefore_model(self, state, runtime, config: RunnableConfig)`
+- Calls `await adispatch_custom_event("summarization", {...}, config=config)` inside
+- `create_agent(model=FakeChatModel, middleware=[probe])`
+- `agent.ainvoke({...}, config={"callbacks": [RecordingHandler()]})`
+
+**Result**:
+
+```
+INFO verify: ProbeMiddleware.abefore_model called
+INFO verify:   config keys: ['callbacks', 'configurable', 'metadata']
+INFO verify:   config.callbacks type: AsyncCallbackManager
+INFO verify:   config.metadata: {'langgraph_step': 1, 'langgraph_node': 'probe.before_model', ...}
+INFO verify: on_custom_event fired: name=summarization
+             run_id=019d7d19-1727-7830-aa33-648ecbee4b95
+             data={'summary': 'fake summary', 'replaced_count': 3}
+SUCCESS: approach A is viable (config injection + adispatch work)
+```
+
+All five predictions held:
+
+1. ✅ `config: RunnableConfig` signature triggers auto-injection despite `trace=False`
+2. ✅ `config.callbacks` is an `AsyncCallbackManager` with `parent_run_id` set
+3. ✅ `adispatch_custom_event(..., config=config)` runs without error
+4. ✅ `RecordingHandler.on_custom_event` receives the event
+5. ✅ The received `run_id` is a valid UUID tied to the running graph
+
+**Bonus finding**: `config.metadata` contains `langgraph_step` and `langgraph_node`. These can be included in the middleware event's metadata to help the frontend position the marker on the timeline.
+
+## 6. Recommended implementation (approach C)
+
+### 6.1 Backend
+
+**New wrapper middleware** in `backend/packages/harness/deerflow/agents/lead_agent/agent.py`:
+
+```python
+from langchain.agents.middleware.summarization import SummarizationMiddleware
+from langchain_core.callbacks import adispatch_custom_event
+from langchain_core.runnables import RunnableConfig
+
+
+class _TrackingSummarizationMiddleware(SummarizationMiddleware):
+    """Wraps upstream SummarizationMiddleware to emit a ``summarization``
+    custom event on every actual summarization, so RunJournal can persist
+    a middleware:summarize row to the event store.
+
+    The upstream class does not emit events of its own. Declaring
+    ``config: RunnableConfig`` in the override lets LangGraph's
+    ``RunnableCallable`` inject the Pregel task config (with callbacks
+    and parent_run_id) regardless of ``trace=False`` on the node.
+    """
+
+    async def abefore_model(self, state, runtime, config: RunnableConfig):
+        before_count = len(state.get("messages") or [])
+        result = await super().abefore_model(state, runtime)
+        if result is None:
+            return None
+
+        new_messages = result.get("messages") or []
+        replaced_count = max(0, before_count - len(new_messages))
+        summary_text = _extract_summary_text(new_messages)
+
+        await adispatch_custom_event(
+            "summarization",
+            {
+                "summary": summary_text,
+                "replaced_count": replaced_count,
+            },
+            config=config,
+        )
+        return result
+
+
+def _extract_summary_text(messages: list) -> str:
+    """Pull the summary string out of the HumanMessage the upstream class
+    injects as ``Here is a summary of the conversation to date:...``."""
+    for msg in messages:
+        if getattr(msg, "type", None) == "human":
+            content = getattr(msg, "content", "")
+            text = content if isinstance(content, str) else ""
+            if text.startswith("Here is a summary of the conversation to date"):
+                return text
+    return ""
+```
+
+Swap the existing `SummarizationMiddleware()` instantiation in `_build_middlewares` for `_TrackingSummarizationMiddleware(...)` with the same args.
+
+**Journal change**: **zero**. `on_custom_event("summarization", ...)` in `journal.py:343-362` already writes both a trace and a `category="middleware"` row.
+
+**History helper change**: extend `_get_event_store_messages` in `backend/app/gateway/routers/threads.py` to surface `category="middleware"` rows as pseudo-messages, e.g.:
+
+```python
+# In the per-event loop, after the existing message branch:
+if evt.get("category") == "middleware" and evt.get("event_type") == "middleware:summarize":
+    meta = evt.get("metadata") or {}
+    messages.append({
+        "id": f"summary-marker-{evt['seq']}",
+        "type": "summary_marker",
+        "replaced_count": meta.get("replaced_count", 0),
+        "summary": (raw or {}).get("content", "") if isinstance(raw, dict) else "",
+        "run_id": evt.get("run_id"),
+    })
+```
+
+The marker uses a sentinel `type` (`summary_marker`) that doesn't collide with any LangChain message type, so downstream consumers that loop over messages can skip or render it explicitly.
+
+### 6.2 Frontend
+
+- `core/messages/utils.ts`: extend the message grouping to recognize `type === "summary_marker"` and yield it as its own group (`"assistant:summary-marker"`)
+- `components/workspace/messages/message-list.tsx`: add a branch in the grouped render switch that renders a distinctive inline card showing `N messages condensed` and a collapsible panel with the summary text
+- No changes to feedback logic: the marker has no `feedback` field so the button naturally doesn't render on it
+
+## 7. Risks
+
+1. **Synchronous path**. The upstream class has both `before_model` and `abefore_model`. Our wrapper only overrides the async variant. If any deer-flow code path ever uses the sync flow, those summarizations won't be captured. Mitigation: also override `before_model` and use `dispatch_custom_event` (sync variant) with the same pattern.
+2. **`_extract_summary_text` fragility**. It depends on the upstream class prefix `"Here is a summary of the conversation to date"` in the injected `HumanMessage`. Any upstream template change breaks detection. Mitigation: pick the first new `HumanMessage` that wasn't in `state["messages"]` before super() — resilient to template wording changes at the cost of a small diff helper.
+3. **`replaced_count` accuracy when concurrent updates**. If another middleware in the chain also modifies `state["messages"]` before super() returns, the naive `before_count - len(new_messages)` arithmetic is wrong. Mitigation: inspect the `RemoveMessage(id=REMOVE_ALL_MESSAGES)` that upstream emits and count from the original input list directly.
+4. **History helper contract change**. Introducing a non-LangChain-typed entry (`type="summary_marker"`) in the `/history` response could break frontend code that blindly casts entries to `Message`. Mitigation: the frontend change above adds an explicit branch; type-check the frontend end-to-end before merging.
+
+## 8. Out of scope / deferred
+
+- Other middleware types (Title, Guardrail, HITL) do not emit custom events either. If we want markers for those too, repeat the wrapper pattern for each. Not in this design.
+- Retroactive markers for old threads (captured before this patch) are impossible without re-running the graph. Legacy threads will show the event-store-recovered messages without a marker.
+- Standard mode (`make dev`) — agent runs inside LangGraph Server, not the Gateway-embedded runtime. `RunJournal` may not be wired there, so the custom event fires but is captured by no one. Tracked as a separate follow-up.
+
+## 9. Next actions
+
+1. Land the current summarize-message-loss fixes (journal `Command` unwrap + event-store-backed `/history` + inline feedback) — implementation verified, being committed now as three commits on `rayhpeng/fix-persistence-new`
+2. Summarize-marker implementation (this spec) → separate follow-up PR based on the above verified design

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

@@ -1,6 +1,6 @@
 import type { Message } from "@langchain/langgraph-sdk";
-import { FileIcon, Loader2Icon } from "lucide-react";
-import { memo, useMemo, type ImgHTMLAttributes } from "react";
+import { FileIcon, Loader2Icon, ThumbsDownIcon, ThumbsUpIcon } from "lucide-react";
+import { memo, useCallback, useMemo, useState, type ImgHTMLAttributes } from "react";
 import rehypeKatex from "rehype-katex";
 
 import { Loader } from "@/components/ai-elements/loader";
@@ -17,6 +17,11 @@ import {
 } from "@/components/ai-elements/reasoning";
 import { Task, TaskTrigger } from "@/components/ai-elements/task";
 import { Badge } from "@/components/ui/badge";
+import {
+  deleteFeedback,
+  upsertFeedback,
+  type FeedbackData,
+} from "@/core/api/feedback";
 import { resolveArtifactURL } from "@/core/artifacts/utils";
 import { useI18n } from "@/core/i18n/hooks";
 import {
@@ -34,16 +39,85 @@ import { CopyButton } from "../copy-button";
 
 import { MarkdownContent } from "./markdown-content";
 
+function FeedbackButtons({
+  threadId,
+  runId,
+  initialFeedback,
+}: {
+  threadId: string;
+  runId: string;
+  initialFeedback: FeedbackData | null;
+}) {
+  const [feedback, setFeedback] = useState<FeedbackData | null>(initialFeedback);
+  const [isSubmitting, setIsSubmitting] = useState(false);
+
+  const handleClick = useCallback(
+    async (rating: number) => {
+      if (isSubmitting) return;
+      setIsSubmitting(true);
+      try {
+        if (feedback?.rating === rating) {
+          await deleteFeedback(threadId, runId);
+          setFeedback(null);
+        } else {
+          const result = await upsertFeedback(threadId, runId, rating);
+          setFeedback(result);
+        }
+      } catch {
+        // Revert on error — feedback state unchanged on catch
+      } finally {
+        setIsSubmitting(false);
+      }
+    },
+    [threadId, runId, feedback, isSubmitting],
+  );
+
+  return (
+    <div className="flex gap-1">
+      <button
+        type="button"
+        className={cn(
+          "text-muted-foreground hover:text-foreground rounded-md p-1 transition-colors",
+          feedback?.rating === 1 && "text-foreground",
+        )}
+        onClick={() => handleClick(1)}
+        disabled={isSubmitting}
+      >
+        <ThumbsUpIcon
+          className={cn("size-4", feedback?.rating === 1 && "fill-current")}
+        />
+      </button>
+      <button
+        type="button"
+        className={cn(
+          "text-muted-foreground hover:text-foreground rounded-md p-1 transition-colors",
+          feedback?.rating === -1 && "text-foreground",
+        )}
+        onClick={() => handleClick(-1)}
+        disabled={isSubmitting}
+      >
+        <ThumbsDownIcon
+          className={cn("size-4", feedback?.rating === -1 && "fill-current")}
+        />
+      </button>
+    </div>
+  );
+}
+
 export function MessageListItem({
   className,
+  threadId,
   message,
   isLoading,
-  threadId,
+  feedback,
+  runId,
 }: {
   className?: string;
+  threadId: string;
   message: Message;
   isLoading?: boolean;
-  threadId: string;
+  feedback?: FeedbackData | null;
+  runId?: string;
 }) {
   const isHuman = message.type === "human";
   return (
@@ -61,7 +135,7 @@ export function MessageListItem({
         <MessageToolbar
           className={cn(
             isHuman ? "-bottom-9 justify-end" : "-bottom-8",
-            "absolute right-0 left-0 z-20 opacity-0 transition-opacity delay-200 duration-300 group-hover/conversation-message:opacity-100",
+            "absolute right-0 left-0 z-20",
           )}
         >
           <div className="flex gap-1">
@@ -72,6 +146,13 @@ export function MessageListItem({
                 ""
               }
             />
+            {feedback !== undefined && runId && threadId && (
+              <FeedbackButtons
+                threadId={threadId}
+                runId={runId}
+                initialFeedback={feedback}
+              />
+            )}
           </div>
         </MessageToolbar>
       )}

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

@@ -18,6 +18,7 @@ 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";
@@ -47,6 +48,8 @@ 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 />;
   }
@@ -58,12 +61,15 @@ export function MessageList({
         {groupMessages(messages, (group) => {
           if (group.type === "human" || group.type === "assistant") {
             return group.messages.map((msg) => {
+              const entry = msg.id ? enrichment?.get(msg.id) : undefined;
               return (
                 <MessageListItem
                   key={`${group.id}/${msg.id}`}
+                  threadId={threadId}
                   message={msg}
                   isLoading={thread.isLoading}
-                  threadId={threadId}
+                  runId={entry?.run_id}
+                  feedback={entry?.feedback}
                 />
               );
             });
@@ -167,7 +173,7 @@ export function MessageList({
               results.push(
                 <div
                   key="subtask-count"
-                  className="text-muted-foreground pt-2 text-sm font-normal"
+                  className="text-muted-foreground font-norma pt-2 text-sm"
                 >
                   {t.subtasks.executing(tasks.size)}
                 </div>,

frontend/src/core/api/feedback.ts

@@ -0,0 +1,42 @@
+import { getBackendBaseURL } from "../config";
+
+import { fetchWithAuth } from "./fetcher";
+
+export interface FeedbackData {
+  feedback_id: string;
+  rating: number;
+  comment: string | null;
+}
+
+export async function upsertFeedback(
+  threadId: string,
+  runId: string,
+  rating: number,
+  comment?: string,
+): Promise<FeedbackData> {
+  const res = await fetchWithAuth(
+    `${getBackendBaseURL()}/api/threads/${encodeURIComponent(threadId)}/runs/${encodeURIComponent(runId)}/feedback`,
+    {
+      method: "PUT",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({ rating, comment: comment ?? null }),
+    },
+  );
+  if (!res.ok) {
+    throw new Error(`Failed to submit feedback: ${res.status}`);
+  }
+  return res.json();
+}
+
+export async function deleteFeedback(
+  threadId: string,
+  runId: string,
+): Promise<void> {
+  const res = await fetchWithAuth(
+    `${getBackendBaseURL()}/api/threads/${encodeURIComponent(threadId)}/runs/${encodeURIComponent(runId)}/feedback`,
+    { method: "DELETE" },
+  );
+  if (!res.ok && res.status !== 404) {
+    throw new Error(`Failed to delete feedback: ${res.status}`);
+  }
+}

frontend/src/core/threads/hooks.ts

@@ -8,6 +8,7 @@ import { toast } from "sonner";
 import type { PromptInputMessage } from "@/components/ai-elements/prompt-input";
 
 import { getAPIClient } from "../api";
+import type { FeedbackData } from "../api/feedback";
 import { fetchWithAuth } from "../api/fetcher";
 import { getBackendBaseURL } from "../config";
 import { useI18n } from "../i18n/hooks";
@@ -294,6 +295,9 @@ export function useThreadStream({
     onFinish(state) {
       listeners.current.onFinish?.(state.values);
       void queryClient.invalidateQueries({ queryKey: ["threads", "search"] });
+      void queryClient.invalidateQueries({
+        queryKey: ["thread-message-enrichment"],
+      });
     },
   });
 
@@ -678,3 +682,65 @@ export function useRenameThread() {
     },
   });
 }
+
+/** Per-message enrichment data attached by the backend ``/history`` helper. */
+export interface MessageEnrichment {
+  run_id: string;
+  /** ``undefined`` = not feedback-eligible; ``null`` = eligible but unrated. */
+  feedback?: FeedbackData | null;
+}
+
+/**
+ * Fetch ``/history`` once and index feedback + run_id by message id.
+ *
+ * Replaces the old ``useThreadFeedback`` hook which keyed by AI-message
+ * ordinal position — an inherently fragile mapping that broke whenever
+ * ``ai_tool_call`` messages were interleaved with ``ai_message`` messages.
+ * Keying by ``message.id`` is stable regardless of run count, tool-call
+ * chains, or summarization.
+ *
+ * The ``/history`` response is refreshed on every stream completion via
+ * ``invalidateQueries(["thread-message-enrichment"])`` in ``onFinish``.
+ */
+export function useThreadMessageEnrichment(
+  threadId: string | null | undefined,
+) {
+  return useQuery({
+    queryKey: ["thread-message-enrichment", threadId],
+    queryFn: async (): Promise<Map<string, MessageEnrichment>> => {
+      const empty = new Map<string, MessageEnrichment>();
+      if (!threadId) return empty;
+      const res = await fetchWithAuth(
+        `${getBackendBaseURL()}/api/threads/${encodeURIComponent(threadId)}/history`,
+        {
+          method: "POST",
+          headers: { "Content-Type": "application/json" },
+          body: JSON.stringify({ limit: 1 }),
+        },
+      );
+      if (!res.ok) return empty;
+      const entries = (await res.json()) as Array<{
+        values?: {
+          messages?: Array<{
+            id?: string;
+            run_id?: string;
+            feedback?: FeedbackData | null;
+          }>;
+        };
+      }>;
+      const messages = entries[0]?.values?.messages ?? [];
+      const map = new Map<string, MessageEnrichment>();
+      for (const m of messages) {
+        if (!m.id || !m.run_id) continue;
+        const entry: MessageEnrichment = { run_id: m.run_id };
+        // Preserve presence: "feedback" key absent → ineligible; present with
+        // null → eligible but unrated; present with object → rated.
+        if ("feedback" in m) entry.feedback = m.feedback;
+        map.set(m.id, entry);
+      }
+      return map;
+    },
+    enabled: !!threadId,
+    staleTime: 30_000,
+  });
+}