* feat(projects): Projects MVP Phase 2 — instructions, document shelf, promotion, trash
Implements docs/superpowers/specs/2026-09-12-projects-mvp-phase2-design.md
(issue #5160, tracker #5129) in the slice order of the spec's §16.
Slices:
- A: ProjectsConfig + write-time 422 UTF-8 byte cap; PROJECT_CONTEXT_KEY
admission pinning (both server-owned sets + worker hoist); latest-only
request-scoped <project> block via DynamicContextMiddleware
wrap_model_call/awrap_model_call (idempotent reassembly, reserved ID
prefix + marker + provenance, never persisted); journal audit
fingerprints; Instructions tab.
- B: ProjectDocumentRow + migration 0023; ProjectDocumentRepository with
locked check-and-set; hash-qualified immutable shelf storage with
Paths helpers; upload/list/content/delete-to-trash routes; project
delete trashes the shelf in-transaction; request-scoped bounded
<documents> index with honest count/shown + actionable overflow note;
list_project_documents/read_project_document tools registered only on
pinned runs; PAT allowlist + drift guards; blocking-IO anchors.
- C: shared thread-upload ingestion service (uploads router refactored to
parity); POST from-thread with provenance; attach-to-thread with
lock-staged copy (archived source allowed); read-only thread-files
view with per-group truncation reporting.
- D: restore (restored/merged/not_found/no_target/content_missing; no
file moves), purge (continuous row lock across unlink/delete/commit,
retryable on FS errors), retention sweep (lazy + startup, 24h orphan
guard, row-side reconciliation never deletes).
- E: Documents tab (shelf + conversation-files browser, provenance,
archived banner, content-missing rows), /workspace/trash route,
sidebar entry, composer attach handoff, i18n (en-US/zh-CN), e2e mocks
+ specs.
Review hardening folded in (10 rounds, all with tests):
- force active shelf content (HTML/XML family) to download; nosniff on
artifact + content responses; unified unsandboxed-iframe PDF preview
(fixes the pre-existing Chromium sandbox blank in the artifact viewer)
- scope document trash to the URL project under the document lock
- atomic no-overwrite filename reservation for ALL ingestion (seeded
claims + os.link commit with suffix retry; same-name re-upload now
unique-names instead of replacing); hidden staging only, no visible
placeholders; lease cleanup on setup failure
- serialize conversion under the document lock with post-lock active
revalidation; drain locked filesystem work on cancellation; preserve
bytes when an insert's commit state is uncertain (including trashed
rows)
- original-integrity checks before serving text or cached conversions;
content_missing surfaced in list responses (UI reads the flag, no
409-probe); downloads always serve original bytes
- bounded streaming document reads with cached char counts; shelf limits
declared in middleware release identity
- thread-root confinement for from-thread sources; config fallback
rejects fractional/infinite values; composer counts staged
attachments; pending attachments persist until submission or removal;
in-flight instruction/rename edits survive save refetches; shelf and
trash pagination; conversation-file and thread-files pages stay
subscribed to refetches
Docs: README/README_zh, backend API.md/ARCHITECTURE.md, AGENTS.md
contracts, config.example.yaml projects block.
Review follow-ups (head b4807477 → this revision):
- The trash retention sweep is split so repeated lazy triggers stay
bounded: the indexed expiry purge still runs on every trigger
(GET /api/trash/documents, POST /api/trash/purge) while the
O(all rows + all files) reconciliation is throttled to one run per
user per 15 minutes (process-local, per-user window). The startup
sweep now runs as a background task instead of blocking gateway
readiness, and shutdown awaits it (bounded).
- The export scrub (stripInternalMarkers) is fence- and indentation-aware
like the render path, so a pasted, fenced <project>/<documents> snippet
survives markdown export while real injected blocks (never fenced) are
still removed. Fence regexes moved to a dependency-free leaf module to
avoid the messages↔streamdown import cycle.
- The artifact viewer's PDF iframe no longer carries an added title
attribute (the upstream e2e contract locates it via :not([title])), and
the upstream artifact-preview spec now pins the new contract: PDFs
render unsandboxed, images keep sandbox="".
* fix(projects): round-2 review — cancel an overrun trash sweep, restore the PDF frame title
- Shutdown cancelled only the shield around the background startup sweep,
so an all-users reconciliation that outlived the 5s budget kept walking
rows and files while the document repo and DB engine were disposed
underneath it. The wait now lives in `_shutdown_startup_trash_sweep`,
which cancels the task and drains it before worker exit: the shield
keeps the wait bounded, the cancel makes it final (CancelledError lands
at the sweep's next await, and `_run_startup_trash_sweep` only catches
`Exception`, so nothing swallows it).
- The browser-preview iframe lost `title={getFileName(filepath)}` in the
previous fix round, leaving the PDF frame without an accessible name
while its siblings keep theirs. Restore it (WCAG frame titles), assert
it in the DOM test, and anchor the e2e on `iframe[title="report.pdf"]`
instead of `iframe:not([title])`.
* fix(projects): round-3 review — report the sweep's late finish, not a phantom cancel
`Task.cancel()` returns False when the sweep already finished inside the
window between the deadline firing and the cancel, so the shutdown log
claimed a cancellation that never happened. Branch on that outcome: the
warning stays for a real cancel, a late finish is logged at info, and both
paths still reap the task before worker exit.
* fix(projects): round-4 review — make Empty trash delete what it confirms
`POST /api/trash/purge` only ran the retention sweep, and the sweep's
candidate selection is age-gated, so a freshly trashed document survived
"Empty trash" even though the confirmation promises that every listed
document is permanently deleted. With one trashed row the route answered
`{"purged": 0}` and left it in place; `GET /api/trash/documents` sweeps
expired rows before listing, so the visible rows were normally ineligible
for the action by construction.
Empty trash now drives `purge_all_trashed`: the caller's trashed rows
(`list_all_trashed`, no age filter) each go through the same guarded,
row-locked `purge` as the single-document delete — bytes first, then the
row, in one transaction — so a row restored mid-flight is skipped instead of
force-deleted, and an unlink failure rolls that row back and answers 500 with
a retryable message. Retention expiry stays where it was: the sweep's
`purge_candidates` is now the only age-gated selection, and the lazy
retention sweep still runs on the listing and at startup.
Tests: the router suite replaces the retention-gated expectation with the
reviewer's repro (fresh row purged, bytes unlinked, shelf and other users'
trash untouched, a failing unlink stays retryable and 500); a blocking-I/O
anchor drives the new entry point through the offload; the mocked e2e covers
the action end to end; a new real-backend spec performs it against the real
gateway and re-reads `GET /api/trash/documents`. README, API, ARCHITECTURE
and the phase-2 design docs (en+zh) state the age-independent contract.
* fix(nginx): defer cors to gateway allowlist
Remove proxy-level wildcard CORS handling so browser origins are controlled by the Gateway allowlist and stay aligned with CSRF origin checks.
* docs: document gateway cors allowlist
Clarify that same-origin nginx access needs no CORS headers while split-origin or port-forwarded browser clients must opt in with GATEWAY_CORS_ORIGINS.
* docs(gateway): record cors source of truth
Document that Gateway CORSMiddleware and CSRFMiddleware share GATEWAY_CORS_ORIGINS as the split-origin source of truth.
* fix(gateway): align cors origin normalization
* docs: clarify gateway langgraph routing
* docs(gateway): update runtime routing note
The tool is registered as `present_files` (plural) in present_file_tool.py,
but four references in documentation and prompt strings incorrectly used the
singular form `present_file`. This could cause confusion and potentially
lead to incorrect tool invocations.
Changed files:
- backend/docs/GUARDRAILS.md
- backend/docs/ARCHITECTURE.md
- backend/packages/harness/deerflow/agents/lead_agent/prompt.py (2 occurrences)
* fix(threads): clean up local thread data after thread deletion
Delete DeerFlow-managed thread directories after the web UI removes a LangGraph thread.
This keeps local thread data in sync with conversation deletion and adds regression coverage for the cleanup flow.
* fix(threads): address thread cleanup review feedback
Encode thread cleanup URLs in the web client, keep cache updates explicit when no thread search data is cached, and return a generic 500 response from the cleanup endpoint while documenting the sanitized error behavior.
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* refactor: extract shared utils to break harness→app cross-layer imports
Move _validate_skill_frontmatter to src/skills/validation.py and
CONVERTIBLE_EXTENSIONS + convert_file_to_markdown to src/utils/file_conversion.py.
This eliminates the two reverse dependencies from client.py (harness layer)
into gateway/routers/ (app layer), preparing for the harness/app package split.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* refactor: split backend/src into harness (deerflow.*) and app (app.*)
Physically split the monolithic backend/src/ package into two layers:
- **Harness** (`packages/harness/deerflow/`): publishable agent framework
package with import prefix `deerflow.*`. Contains agents, sandbox, tools,
models, MCP, skills, config, and all core infrastructure.
- **App** (`app/`): unpublished application code with import prefix `app.*`.
Contains gateway (FastAPI REST API) and channels (IM integrations).
Key changes:
- Move 13 harness modules to packages/harness/deerflow/ via git mv
- Move gateway + channels to app/ via git mv
- Rename all imports: src.* → deerflow.* (harness) / app.* (app layer)
- Set up uv workspace with deerflow-harness as workspace member
- Update langgraph.json, config.example.yaml, all scripts, Docker files
- Add build-system (hatchling) to harness pyproject.toml
- Add PYTHONPATH=. to gateway startup commands for app.* resolution
- Update ruff.toml with known-first-party for import sorting
- Update all documentation to reflect new directory structure
Boundary rule enforced: harness code never imports from app.
All 429 tests pass. Lint clean.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* chore: add harness→app boundary check test and update docs
Add test_harness_boundary.py that scans all Python files in
packages/harness/deerflow/ and fails if any `from app.*` or
`import app.*` statement is found. This enforces the architectural
rule that the harness layer never depends on the app layer.
Update CLAUDE.md to document the harness/app split architecture,
import conventions, and the boundary enforcement test.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* feat: add config versioning with auto-upgrade on startup
When config.example.yaml schema changes, developers' local config.yaml
files can silently become outdated. This adds a config_version field and
auto-upgrade mechanism so breaking changes (like src.* → deerflow.*
renames) are applied automatically before services start.
- Add config_version: 1 to config.example.yaml
- Add startup version check warning in AppConfig.from_file()
- Add scripts/config-upgrade.sh with migration registry for value replacements
- Add `make config-upgrade` target
- Auto-run config-upgrade in serve.sh and start-daemon.sh before starting services
- Add config error hints in service failure messages
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* fix comments
* fix: update src.* import in test_sandbox_tools_security to deerflow.*
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* fix: handle empty config and search parent dirs for config.example.yaml
Address Copilot review comments on PR #1131:
- Guard against yaml.safe_load() returning None for empty config files
- Search parent directories for config.example.yaml instead of only
looking next to config.yaml, fixing detection in common setups
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* fix: correct skills root path depth and config_version type coercion
- loader.py: fix get_skills_root_path() to use 5 parent levels (was 3)
after harness split, file lives at packages/harness/deerflow/skills/
so parent×3 resolved to backend/packages/harness/ instead of backend/
- app_config.py: coerce config_version to int() before comparison in
_check_config_version() to prevent TypeError when YAML stores value
as string (e.g. config_version: "1")
- tests: add regression tests for both fixes
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix: update test imports from src.* to deerflow.*/app.* after harness refactor
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
- Add README.md with project overview, quick start, and API reference
- Add CONTRIBUTING.md with development setup and contribution guidelines
- Add docs/ARCHITECTURE.md with detailed system architecture diagrams
- Add docs/API.md with complete API reference for LangGraph and Gateway
- Add docs/README.md as documentation index
- Update CLAUDE.md with improved structure and new features
- Update docs/TODO.md to reflect current status
- Update pyproject.toml description
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
