* fix(client): stop embedded uploads from writing through symlinks
DeerFlowClient.upload_files copied each file with shutil.copy2 and let
convert_file_to_markdown write the companion straight into the uploads
directory. Local and AIO sandboxes can write to that directory, so a
symlink planted at an upload name or at the companion's name was
followed: the upload's bytes and the converted Markdown landed in
whatever host file the link pointed to, and the call reported success.
The Gateway refuses symlinked destinations and the IM channels write
through write_upload_file_no_symlink; the embedded client never adopted
either.
Uploads now go through copy_upload_file_no_symlink, a new helper next
to write_upload_file_no_symlink. It keeps copy2's content, permission
bits and timestamps, so files stay readable to Docker sandboxes, but
applies them to the descriptor opened with O_NOFOLLOW and opens the
source first so a missing source cannot truncate an existing upload.
As in the Gateway, a file with an unsafe destination is skipped and
listed in skipped_files, success turns false, and the message says how
many were skipped. The companion is converted inside a private temporary
directory and then written with write_upload_file_no_symlink; one whose
name is unsafe is left out like a failed conversion, and the original
upload is kept.
* docs(changelog): note embedded upload symlink fix (#5578)
* fix(client): keep copy2's same-file guard and companion permissions
Review follow-up. Two regressions in the previous commit.
copy_upload_file_no_symlink opened the destination before comparing it
with the source, and that open truncates. Passing a file that already
sits in the thread's uploads directory therefore copied an emptied file
over itself: the upload reported success with size 0 and the original
bytes were gone, where copy2 raised SameFileError and left the file
alone. The destination is now compared with the source through
os.path.samestat before anything is opened, so identity — including a
hardlink or another spelling of the same path — raises SameFileError as
before.
The Markdown companion was published with write_upload_file_no_symlink,
which creates a new file as 0600 and ignores the converted file's mode.
Under umask 022 the companion became 0600 while its own document stayed
0644, so a bind-mounted sandbox running as another uid could read the
upload but not the Markdown the response advertises. It now goes
through the same copy helper as the upload, which preserves the
converter's permission bits.
* fix(uploads): delete the requested upload, not a symlink's target
delete_file_safe resolved the requested path before unlinking it. The
uploads directory is writable from local and AIO sandboxes, so a
symlink planted under an upload name was followed: deleting alias.pdf
removed the victim.pdf it pointed to, and the companion cleanup then
removed victim.md, while the link itself survived and the call reported
"Deleted alias.pdf". A link resolving outside the directory was already
refused by the traversal check, so the damage stayed inside the
thread's uploads.
The function now checks and unlinks the requested entry itself and
treats a symlink as not found, the same way list_files_in_dir already
hides it. unlink() never follows the final component, so a file swapped
for a link between the check and the unlink removes only the link.
Tests cover the helper, the Gateway DELETE route, and
DeerFlowClient.delete_upload.
* docs(changelog): note upload delete symlink fix (#5547)
* feat(tools): filter list_uploaded_files by name and extension
Add optional query and extensions so historical upload discovery can
find older matching files instead of dropping them behind the default
20-item mtime cap.
Fixes#5339
* fix(tools): strip glob stars from list_uploaded_files extensions
Model-supplied tokens like *.pdf were prefixed to .*.pdf and never
matched Path.suffix. Also run ruff format so the backend format gate
passes.
* 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>
