* feat(uploads): inject document outline into agent context for converted files
Extract headings from converted .md files and inject them into the
<uploaded_files> context block so the agent can navigate large documents
by line number before reading.
- Add `extract_outline()` to `file_conversion.py`: recognises standard
Markdown headings (#/##/###) and SEC-style bold structural headings
(**ITEM N. BUSINESS**, **PART II**); caps at 50 entries; excludes
cover-page boilerplate (WASHINGTON DC, CURRENT REPORT, SIGNATURES)
- Add `_extract_outline_for_file()` helper in `uploads_middleware.py`:
looks for a sibling `.md` file produced by the conversion pipeline
- Update `UploadsMiddleware._create_files_message()` to render the outline
under each file entry with `L{line}: {title}` format and a `read_file`
prompt for range-based reading
- Tests: 10 new tests for `extract_outline()`, 4 new tests for outline
injection in `UploadsMiddleware`; existing test updated for new `outline`
field in `uploaded_files` state
Partially addresses #1647 (agent ignores uploaded files).
* fix(uploads): stream outline file reads and strip inline bold from heading titles
- Switch extract_outline() from read_text().splitlines() to open()+line iteration
so large converted documents are not loaded into memory on every agent turn;
exits as soon as MAX_OUTLINE_ENTRIES is reached (Copilot suggestion)
- Strip **...** wrapper from standard Markdown heading titles before appending
to outline so agent context stays clean (e.g. "## **Overview**" → "Overview")
(Copilot suggestion)
- Remove unused pathlib.Path import and fix import sort order in test_file_conversion.py
to satisfy ruff CI lint
* fix(uploads): show truncation hint when outline exceeds MAX_OUTLINE_ENTRIES
When extract_outline() hits the cap it now appends a sentinel entry
{"truncated": True} instead of silently dropping the rest of the headings.
UploadsMiddleware reads the sentinel and renders a hint line:
... (showing first 50 headings; use `read_file` to explore further)
Without this the agent had no way to know the outline was incomplete and
would treat the first 50 headings as the full document structure.
* fix(uploads): fall back to configurable.thread_id when runtime.context lacks thread_id
runtime.context does not always carry thread_id (depends on LangGraph
invocation path). ThreadDataMiddleware already falls back to
get_config().configurable.thread_id — apply the same pattern so
UploadsMiddleware can resolve the uploads directory and attach outlines
in all invocation paths.
* style: apply ruff format
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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>
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Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
SHIYAO ZHANG
DanielWalnut