* feat(skills): per-user skill isolation (#2905)
Implement user-scoped skill storage that isolates custom skills between
users while sharing public skills globally.
Key changes:
- Add UserScopedSkillStorage class for per-user custom skill directories
- Introduce get_or_new_user_skill_storage() factory with user_id context
- Auth middleware sets effective_user_id for request-scoped storage
- Agent/prompt/middleware now use user-scoped storage and prompt cache
- Sandbox mounts user-scoped skill directories for search/read tools
- Add validate_skill_file_path() to SkillStorage for path security
- Migration script supports --all-users bulk migration
- Frontend: add editable field to Skill type, error check in enableSkill
- All skill categories can be toggled (custom skills default to enabled)
- Update skill-creator SKILL.md with isolation-aware instructions
Tests:
- Add test_user_scoped_skill_storage.py (new)
- Update all existing skill tests for user-scoped storage
- Update sandbox, client, and router tests
* fix(skills): address second-round PR review feedback (#3889)
- P1-1: restrict legacy skill mount to users without custom skills
- P1-2: fail-closed for _is_disabled_skill_path (OSError → return True)
- P2-1: AND-merge global extensions_config skill disabled state
- P2-2: atomic write for _skill_states.json (mkstemp + replace)
- P2-3: normalize X-DeerFlow-Owner-User-Id in trusted boundary
- P2-4: LRU-bounded _enabled_skills_by_config_cache (OrderedDict, maxsize=256)
- P2-5: clear global prompt cache on PUBLIC skill toggle
- P2-6: invalidate skill caches on client.update_skill
* fix(tests): correct tool policy test after merge
* fix(skills): use DEFAULT_SKILLS_CONTAINER_PATH in UserScopedSkillStorage
The "/mnt/skills" literal in UserScopedSkillStorage.__init__ triggers
test_skill_container_path_defaults::test_mnt_skills_literal_is_owned_by_skill_constants_module
on CI. Migrate the default to the existing deerflow.constants constant,
matching the pattern already used by LocalSkillStorage, SkillStorage, and
the durable/tool_error middlewares.
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* feat(mcp): add per-server tool_call_timeout for MCP tool calls
Add a configurable timeout for individual MCP tool calls to prevent
agent runs from blocking indefinitely when an MCP server becomes
unresponsive (e.g., rate-limited HTTP API, hung subprocess).
Uses the MCP SDK's built-in read_timeout_seconds parameter on
ClientSession.call_tool, which handles the timeout within the
session's own task — avoiding cross-task cancellation issues with
the session pool (ref #3379, #3203).
Config field is named tool_call_timeout (not timeout) to avoid
collision with langchain-mcp-adapters' existing timeout field on
HTTP/SSE connections.
Closes#3840
* fix(mcp): read tool_call_timeout from McpServerConfig, not connection dict
The previous implementation put tool_call_timeout into the connection dict
returned by build_server_params, which langchain's create_session then
passed to _create_stdio_session(), causing TypeError. Now reads the timeout
directly from ExtensionsConfig.mcp_servers where the wrapper is built,
keeping it out of the connection dict entirely.
Fixes P1 bug from review on #3843.
* test(mcp): regression test for tool_call_timeout not leaking into connection dict
Adds two tests:
- test_build_server_params_excludes_tool_call_timeout: verifies the connection
dict returned by build_server_params() does NOT contain tool_call_timeout
- test_stdio_tool_call_timeout_does_not_raise_typeerror: end-to-end test that
get_mcp_tools() with a stdio server having tool_call_timeout configured loads
tools without TypeError from _create_stdio_session()
Regression for PR #3843 P1 bug.
* fix(mcp): only pass read_timeout_seconds when tool_call_timeout is set
When tool_call_timeout is None, don't pass read_timeout_seconds=None to
session.call_tool(). This avoids breaking existing tests that assert on
exact call_tool arguments without the extra kwarg.
* docs(mcp): clarify stdio tool timeout
The official MCP configuration schema uses `transport` to specify the
transport mechanism (stdio/sse/http), but `McpServerConfig` only honored
`type` and defaulted to `stdio`. Remote MCP servers configured with just
`transport: sse` were therefore misidentified as stdio and failed with
"with stdio transport requires 'command' field".
Add a model validator that promotes `transport` to `type` when only
`transport` is provided, while keeping `type` authoritative when both
are set. This matches the MCP-spec field name without breaking existing
configurations.
Fixes#3238
* Fix env resolution in MCP config lists
* fix:unset env variable and consistent function
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* fix(harness): resolve runtime paths from project root
* docs(config): update
* fix(config): address runtime path review feedback
* test(config): fix skills path e2e root
* test(config): cover legacy config fallback when project root lacks config files
Verifies that when DEER_FLOW_PROJECT_ROOT is unset and cwd has no
config.yaml/extensions_config.json, AppConfig and ExtensionsConfig fall back
to the legacy backend/repo-root candidates — the backward-compat path
requested in PR #2642 review.
---------
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>
