Toggling a skill wrote resolved secrets into extensions_config.json. The
Gateway skill toggle and DeerFlowClient.update_skill loaded the file with
ExtensionsConfig.from_file(), which replaces every "$VAR" string with the
environment value (and an unset variable with ""), then serialized that
model back through to_file_dict(). A "$GITHUB_TOKEN" reference was
persisted as the plaintext token, and an unset reference was erased for
good. DeerFlowClient.update_mcp_config had the same flaw for every key
other than mcpServers.
Every writer now does a raw read-modify-write, the way the MCP router
already did: read_raw_extensions_config reads the on-disk JSON,
set_raw_skill_enabled changes only the target entry, and
validate_raw_extensions_config checks the candidate the way the runtime
will load it before the atomic write. When the file does not exist yet,
the Gateway seeds it with the cached skill states only, never the
resolved cached model. The MCP router's raw loader and candidate
validation delegate to the same helpers, so the rule lives in one place,
and to_file_dict() is removed so the unsafe serialization has no entry
point left.
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* feat(extensions): allow constructor kwargs on config-declared middlewares
extensions.middlewares entries may be a class-path string or {class, kwargs}.
String entries keep the zero-argument constructor. Unknown fields and blank
class paths fail at config validation. Constructor errors still fail at
agent creation.
Fixes#5311
* fix(extensions): coerce middleware kwargs to JSON types
YAML timestamps became datetime objects while JSON kept strings, so
constructors and to_file_dict() json.dump saw different types. Validate
kwargs as JSON types at config load, stringify dates, reject NaN and
other non-JSON values, and cover the raw-dict loader branch.
* style(extensions): wrap middleware Field description for ruff E501
make lint failed: the middlewares description was 289 chars (limit 240).
Wrap it and run ruff format on the two files this PR last touched.
* docs: compact configured middleware guidance to satisfy size limit
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* feat(mcp): map request-scoped secrets to HTTP/SSE headers
`user_auth` binds a credential to a configured DeerFlow user, so a caller
that picks the credential per request — a multi-tenant gateway, a per-run
API key, one shared MCP server fronting several environments — had to
register one MCP server entry per credential.
Add a declarative `mcpServers.<server>.headers_from_context` block mapping
HTTP header names to keys of the run request's `config.context.secrets`
carrier. A new built-in interceptor resolves the mapping on every tool call
and rewrites those headers, mirroring `user_scoped_auth`. The config file
stores names only, never a credential, so the Gateway returns the block
unmasked.
Registered after OAuth and `user_auth` in the interceptor chain: the later
interceptor runs closer to the transport, and the value chosen for this one
request is the most specific, so it wins. Fail-closed by default — a mapped
key missing from the request raises a `ToolException` naming only that key,
because falling back to the server's discovery credential would send one
tenant's call under another tenant's authority. `on_missing: "passthrough"`
opts out.
Durable background tasks are excluded: `McpTaskToolCaller` drives status and
cancel polls after the Agent run ends, where no run context exists, so the
fail-closed interceptor would deny every poll. Those calls keep using
server-level credentials, and a server declaring both `headers_from_context`
and `task_toolsets` now logs a warning.
Also corrects the custom-interceptor example in docs/MCP_SERVER.md (and the
matching claim in skills/AGENTS.md), which read request secrets from
`langgraph.config.get_config()["context"]`. That key is `None` inside a tool
call — the run context rides the LangGraph runtime, not the RunnableConfig
propagated to child runnables — so interceptors written from that example
never saw a value. The example now reads `request.runtime`, and
tests/test_mcp_context_headers.py pins LangGraph's runtime-injection rule by
driving a real langchain-mcp-adapters tool through a real graph with the
ambient-runtime fallback disabled.
Closes#5005
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* fix(mcp): resolve credential headers case-insensitively, carry them on durable submit
Review follow-ups on `headers_from_context`.
HTTP field names are case-insensitive, but every dict on the path to the wire
is not: `build_server_params` copies the operator's static `headers` spelling
verbatim, and langchain-mcp-adapters merges interceptor overrides into the
connection with a plain `{**connection_headers, **override_headers}` splat. A
static `authorization` and an injected `Authorization` therefore both reached
httpx as separate field lines, and a server reading the field with a
single-value accessor got the static discovery credential — inverting the
documented `headers` < `oauth` < `user_auth` < `headers_from_context`
precedence and running a per-request call under the shared credential.
Normalizing inside the interceptor cannot fix that on its own: the adapter
builds the request with `headers=None`, so an interceptor never sees the
connection's static headers and cannot displace them however it spells its own
key. A new `mcp/headers.py::apply_header_overrides` therefore drops any key
differing only in case and emits the spelling the connection already uses.
Applied to `headers_from_context`, `user_auth`, the OAuth interceptor, the
OAuth discovery-header write, and the durable-task connection merge, which all
carried the same collision. `headers_from_context.headers` now also rejects one
header mapped under two spellings at config load, in both the harness model and
the Gateway mirror.
Durable submit now carries the mapped headers, as docs/MCP_SERVER.md already
promised. `McpTaskToolCaller` disabled the interceptor for the whole caller, but
that caller serves submit as well as the polls, and submit is awaited inline
inside the Agent's tool call — where the run's LangGraph runtime is still the
ambient contextvar, so no secret has to be threaded through `TaskSubmitRequest`
or reach durable storage. The caller builds one chain and keeps a second view of
it without the context-headers interceptor; `call_tool` takes
`request_scoped_headers`, set only by `OrdinaryMcpTaskDriver.submit`. Status and
cancel keep server-level credentials, so background polls still cannot fail
closed, and the startup warning now describes the half it actually covers.
`_merge_preserving_secrets` restores masked extras inside `headers_from_context`
instead of writing the `***` sentinel back over the stored value, matching the
treatment `user_auth` extras and server-level extras already get; extras a PUT
omits carry over as well, while the declared mapping still replaces verbatim so
a round trip can remove an entry. `extra="allow"` plus name-based sensitivity
detection means the usual casualty is a name-valued key such as `tokenHeader`,
not only a credential.
The existing override test seeded the static header onto `request.headers`,
which production never does, so it modelled a merge that really happens one
layer down; the new tests drive a real adapter tool through a real connection
and assert on the headers the session is opened with, and the durable-submit
test runs through a real tool node with no runtime patching.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* fix(mcp): reject case-insensitive duplicate static header names
* fix(mcp): preserve omitted headers_from_context fields on partial updates
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
* feat(mcp): per-user credential injection for shared MCP servers
A single HTTP/SSE MCP server entry can now serve several users, each
authenticated to the remote service with their own credential. A server
opts in with a user_auth block mapping user ids to credential header
values ($ENV_VAR references supported):
"user_auth": {
"header": "Authorization",
"users": { "<user-id>": "$SERVICE_TOKEN_ALICE" }
}
The built-in user-scoped auth interceptor resolves the authenticated
runtime user on every tool call (request runtime -> ambient LangGraph
runtime -> auth config -> request-scoped user ContextVar) and rewrites
the configured header via request.override(), the same per-call
mechanism as the OAuth interceptor. It registers after OAuth in the
shared assembly so its per-user value wins the header when a server
declares both. The entry's static headers are used only for startup
tool discovery.
Fail-closed by default: an unmapped user - including the anonymous
default-user fallback - or a credential whose env reference resolved
empty gets an actionable ToolException instead of another user's
credential; on_missing: "passthrough" opts out per server. Combined
with the existing per-(user, thread) MCP session scoping this gives
credential isolation on shared servers.
Gateway API: user_auth.users values are masked in GET responses, and
PUT round-trips preserve stored credentials for masked values (same
contract as env/headers/oauth secrets); a masked value for a user id
not already stored is rejected.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(mcp): address review — preserve stored user_auth sub-fields on partial PUT, warn-and-skip stdio, allow extras
Review findings from #4868:
1. A partial user_auth payload (e.g. {"enabled": false}) merged to
users={} and default on_missing, irreversibly wiping stored
credentials on PUT. The merge is now sub-field-aware via
model_fields_set — omitted sub-fields carry the stored values, an
explicitly sent users map still replaces (so full-round-trip removal
works), masked values still swap back for stored credentials.
2. user_auth on a stdio server was a silent no-op: rewritten headers go
to call meta, never a transport header, while deny errors still fired.
The interceptor builder now warns and skips non-sse/http servers,
matching the tool_call_timeout transport-mismatch convention.
3. McpUserScopedAuthConfigResponse now allows extra keys like the
harness-side model, and extras survive masking and merge, matching
the server-level model_extra handling.
Adds four regression tests (partial-PUT preservation, explicit-map
replacement, extras round-trip, stdio warn-and-skip).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(mcp): reject blank user_auth.header at the gateway
A blank header passed the gateway response model, was persisted, then
failed the harness-side ExtensionsConfig validator on reload — the PUT
returned 500 after the write and every later config load/startup failed
until the file was hand-edited. Mirror the harness non-blank validator
on McpUserScopedAuthConfigResponse so the PUT fails with 422 before
anything is written.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* style: ruff format extensions_config.py
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(mcp): harden the trust chain and masking around user-scoped credential selection
Address review round 4:
- Scrub client-supplied user_id from run context/configurable for
external callers in inject_authenticated_user_context, before every
early return, and restamp only from request.state.user. Now that
user_id selects which user's credential user-scoped MCP auth injects,
a forged value must not survive any future path that skips the
restamp. Internal callers (IM channels, scheduler) keep supplying
end-user identity as before (PR #3294 contract). Regression tests pin
both the scrub and that a forged body.context.user_id can never
resolve as another user through merge + inject ordering.
- Include the caller's own resolved user id in the fail-closed deny
message so operators can copy the exact users key (it differs by
deployment path), and document the key formats in the mcp.mdx doc.
- Mask sensitive extra keys inside user_auth on GET like server-level
extras, and swap masked sentinels back for stored values on PUT via
_merge_extra_value_preserving_masked.
- Extract the interceptor wrap loop into compose_tool_interceptors and
pin the security property functionally: an OAuth interceptor that
actually sets Authorization loses the final header to the per-user
credential through the same composition the session-pool path uses.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* fix(docker): let the Gateway write extensions_config.json in production
AGENTS.md states extensions_config.json may be edited at runtime through the
Gateway API, and the Gateway implements that for the MCP enable switch,
PUT/PATCH /api/mcp/config and the skill update route. Two properties of the
production compose stack made every one of those writes fail:
- the file was mounted read-only, and
- Docker mounts it as its own mount point, so the temp-file-plus-rename in
atomic_write_extensions_config hit EBUSY. Linux refuses rename() over a
mount point whether or not the mount is writable, so making the mount
read-write alone is not enough.
Mount it read-write and fall back to an in-place overwrite on EBUSY only.
The fallback is deliberately non-atomic and says so in a warning; it is
reached only where the atomic route cannot work, and any other errno still
propagates. config.yaml stays read-only: no API writes it.
docker-compose-dev.yaml mounts the whole project directory, so the
destination is an ordinary file there and this never surfaced in development.
* test(docker): parse mount options instead of matching a :ro suffix
Docker's short-syntax options segment is comma-separated, so a read-only
mount can legally be spelled ":ro,z" or ":z,ro" — common with SELinux
relabelling. Matching the raw string for a ":ro" suffix reads those as
writable, which silently defeats the guard: the writability assertion would
pass on a read-only mount, and the config.yaml assertion would fail on a
correctly read-only one.
Parse the options segment and test membership instead, and cover the parser
with the spellings that broke the suffix check.
* fix(config): harden mutable extensions config
* feat(mcp): add durable task runtime foundation
* fix(chart): sync embedded config version
* fix(mcp): isolate task polls during shutdown
* feat(mcp): track consecutive poll errors on mcp_tasks
poll_attempt_count grows on every claim (successful polls included), so it
cannot drive a failure backoff without misjudging normal long tasks. Add
consecutive_poll_error_count: incremented when a claim is released after a
poll error, reset to zero by any applied snapshot. The backoff/terminal
policy that consumes it lands with the first concrete driver.
* fix(mcp): harden durable task lifecycle
* feat(mcp): add ordinary durable task driver
* test(mcp): address durable task review feedback
* fix(mcp): preserve submit tool descriptions
* fix(mcp): bound remote task calls
* fix(mcp): bound persisted task payloads
* fix(mcp): preserve task tool error details
* fix(mcp): enforce durable task boundaries
* test(mcp): cover task config snapshot lifecycle
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* fix: bound MCP server bring-up timeouts and exclude externalized tool outputs from delivery verification
Two related robustness fixes:
1. MCP server bring-up was unbounded. tool_call_timeout only covered
session.call_tool(); tool discovery (subprocess spawn + initialize +
tools/list) and persistent stdio session initialization could hang
forever, blocking agent construction (and on the Gateway event loop,
the whole process). Add a per-server session_init_timeout
(default DEFAULT_MCP_SESSION_INIT_TIMEOUT = 60s, null disables) that
bounds both discovery and pooled-session initialization. The session
pool's existing cancellation handling tears down a session stuck
mid-creation in its own task.
2. ToolOutputBudgetMiddleware externalizes oversized tool outputs into
outputs/.tool-results/ (configurable tool_output.storage_subdir). The
workspace-change scanner and run delivery verification counted those
files as produced artifacts, so any run that externalized a tool output
without also presenting a real artifact failed with
"Artifact delivery incomplete". Exclude TOOL_RESULTS_DIRNAME via a
shared constant (mirroring BROWSER_FRAMES_DIRNAME) and thread the
configured storage_subdir through snapshot capture so both
workspace-changes events and delivery verification stay clean.
* review: enforce single-segment tool_output.storage_subdir; document discovery-timeout cleanup
Address review feedback:
1. A custom tool_output.storage_subdir with a path separator (e.g.
cache/tool-results) silently no-oped the workspace-scanner exclusion:
os.walk yields one-segment dirnames, so a nested value never matched and
its files were counted as produced artifacts again. ToolOutputConfig now
validates storage_subdir as a single directory name (rejects separators,
.., absolute, empty) with tests, so the exclusion is always sound.
2. The discovery-timeout path now documents why cancellation is safe, mirroring
the session-init note: discovery runs inside the adapter's nested async
context managers, and stdio_client's finally terminates the process tree
(SIGTERM->SIGKILL on POSIX, process-tree on Windows), so a timed-out npx
subprocess and its children are reaped rather than accumulating.
* review: log session-init timeouts and align API response model default with runtime config
Address second-round review feedback:
1. A session-init timeout raised TimeoutError without any log, unlike the
discovery timeout which logs a WARNING. Wrap the bounded get_session in a
try/except that logs the timeout (server name + seconds) and re-raises, so
operators can diagnose tool-call failures caused by hung MCP sessions.
2. McpServerConfigResponse.session_init_timeout defaulted to None while
McpServerConfig defaults to 60s: a server created via PUT /api/mcp/config
without the field was persisted with null (no timeout) while the same
server created in the config file got 60s. Align the response-model default
to DEFAULT_MCP_SESSION_INIT_TIMEOUT so API-created and file-created servers
behave the same; an explicit null still opts out.
* review: narrow the discovery-timeout handler to the bounded wait_for path
The except TimeoutError clause covered both the bounded wait_for branch and
the bare discovery branch. With session_init_timeout opted out (None), a
TimeoutError raised by discovery itself would hit the %.1f format with None:
logging raises TypeError internally, the WARNING is silently dropped, and a
--- Logging error --- traceback goes to stderr.
Narrow the handler to wrap only the wait_for call, where the branch condition
guarantees the timeout value is not None. A discovery-internal TimeoutError on
the opted-out path now falls through to the generic failure handler and is
reported as 'tool discovery failed' with exc_info. Covered by a regression
test that asserts the skip is reported without any broken format.
* fix(skills): offload update_skill's blocking IO and share the config write lock
Re-applied on top of main rather than merged: update_skill has since gained
admin gating, user-scoped storage and a PUBLIC vs CUSTOM/LEGACY split, so the
offload is applied per path.
- PUBLIC: the extensions_config.json read-modify-write (path resolve, snapshot,
merge, write, reload) moves to a worker thread via asyncio.to_thread. The
payload is built from a snapshot so the cached singleton is never mutated in
place while the write is still in flight.
- CUSTOM/LEGACY: set_skill_enabled_state is offloaded; the non-user-scoped
fallback takes the same shared-file RMW path as PUBLIC.
- Both load_skills calls (and storage construction) are offloaded.
The RMW lock now lives next to reload_extensions_config as
get_extensions_config_write_lock() and is acquired by both the skills router and
the MCP router, which performs the same read-modify-write on the same file.
Previously each router held its own module-local lock, so once both sides
offloaded, a PUT /api/mcp/config could run inside a skill toggle's read->write
window and the later write would silently drop the other's change.
The lock is keyed by the running event loop rather than being a module-level
singleton: asyncio primitives bind to the first loop that awaits them, which
makes a plain module-level lock unusable in a process that runs more than one
loop.
Adds a cross-router regression anchor asserting a skill toggle and an MCP update
never overlap inside the RMW (max in-flight 1); it observes 2 when the routers
use separate locks.
* fix(config): own the extensions_config RMW lock from the worker thread
An asyncio.Lock held around `await asyncio.to_thread(...)` protects only the
awaiting task. If that task is cancelled the context manager releases the lock
immediately while Python keeps running the worker thread, so a second skills or
MCP writer could acquire it and operate on extensions_config.json concurrently
with the first worker — reopening the lost-update window this was meant to close.
The per-event-loop keying had a second hole: writers on different loops got
different locks and so did not exclude each other at all.
Replace it with a process-wide threading.Lock acquired *inside* the worker that
performs the RMW (`_write_extensions_skill_state` and `_apply_mcp_config_update`),
so ownership belongs to the thread doing the writing and is held until the write
and reload actually finish, regardless of what happens to the caller. A
threading.Lock also has no event-loop affinity.
Adds a cancellation regression: the skills worker is paused inside the lock, its
route task is cancelled, and the MCP writer is started — the MCP RMW must not
enter until the skills worker is released. Against the previous asyncio-lock
design this test fails with ['skills-enter', 'mcp-enter'].
The two existing serialization tests instrumented by replacing the worker
functions, which now bypasses the lock under test; they instead patch inside the
real workers (each module's reload_extensions_config, the last step under the
lock) so the production lock is exercised.
---------
Co-authored-by: ly-wang19 <ly-wang19@users.noreply.github.com>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* feat: add lark cli integration
* fix: polish lark integration actions
* feat: support lark incremental permissions
* fix: detect lark authorization completion
* fix: harden lark integration install
* feat: expand lark auth scopes and reuse host auth in sandbox
Default lark auth to least-privilege (recommend=false, base sign-in only)
and expose the full set of lark-cli --domain business domains as native
--domain grants instead of a 4-domain read-only mapping. Resolve the
skill pack from the latest larksuite/cli GitHub release at install time
with content-hash integrity, and surface version/runtime drift in status.
Share the per-user lark-cli config/data profile between the Gateway
Settings auth flow and agent conversations by mounting the integration
dirs into the AIO sandbox and injecting the matching env for lark-cli
commands, with an allowlisted extra_mounts path in the provisioner/K8s
backend and traversal guards on integration paths.
* style: fix lint issues from ruff and prettier
Sort imports in the provisioner PVC test and re-wrap two long i18n
description strings to satisfy backend ruff and frontend prettier CI.
* fix(lark): address managed integration review feedback
* fix(frontend): stabilize integrations settings e2e
* test(sandbox): isolate remote backend legacy visibility check
* test: fix backend unit failures after merge
* Harden Lark integration review fixes
* Format Lark integration E2E test
* fix(lark): harden sandbox credential exposure and status disclosure
Address willem_bd's security review on PR #3971:
- Mount the per-user lark-cli config dir (long-lived appSecret) read-only
into the AIO sandbox; only the refreshable-token data dir stays writable.
- Redact host filesystem paths (install_path, cli.path) from
GET /lark/status and the config/auth complete responses for non-admin
callers, fail-closed on any auth error.
- Document the npm postinstall trade-off (--ignore-scripts is not viable
because @larksuite/cli fetches its platform binary in postinstall).
- Document the sandbox credential trust boundary in AGENTS.md and README,
pointing at the sidecar-broker follow-up (#4338).
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* fix(config): close out #4124 review follow-ups
Extracts the (mtime, size, sha256) content-signature helper that was
duplicated between config/app_config.py and mcp/cache.py into a new
config/file_signature.py, and fixes ExtensionsConfig.resolve_config_path()
to return None instead of raising FileNotFoundError when an explicit
config_path argument or DEER_FLOW_EXTENSIONS_CONFIG_PATH points at a file
that has since been deleted -- the exact resolution mode Docker dev/prod
uses per AGENTS.md, so the MCP tools-cache staleness check could raise
instead of degrading to "not stale". Both were flagged by willem-bd in
review on #4124 and explicitly deferred there ("flagging for visibility",
"leaving the extraction as the follow-up you suggested").
* fix(config): keep explicit extensions-config paths fail-loud
resolve_config_path() previously turned every missing-file case into a
clean None, including an explicit config_path argument or
DEER_FLOW_EXTENSIONS_CONFIG_PATH (the exact mode Docker dev/prod uses).
That silently downgrades a bad Docker mount, typo, or deleted
production config to "no extensions" instead of surfacing the
misconfiguration, per fancyboi999's review [P1] and willem-bd's
follow-up notes on this PR.
Restores FileNotFoundError for the two explicit modes (config_path
argument, DEER_FLOW_EXTENSIONS_CONFIG_PATH); only the fallback search
mode (no explicit path/env var, nothing found in the usual locations)
still returns None, since that is the legitimate "extensions were
never configured" case.
The one caller that needs the old fail-soft behavior -- the MCP
tools-cache staleness check, which re-resolves the path on every
get_cached_mcp_tools() call -- gets a narrow, local catch instead
(deerflow.mcp.cache._resolve_config_path) so a config file going
missing mid-run still degrades the cache to "not stale" rather than
crashing a hot per-request path. Also hoists the double os.getenv()
read in the env-var branch into a local, per willem-bd's nit.
Adds resolver-level tests for both explicit-path and env-var raises,
a dedicated search-mode None regression test, and updates the
existing MCP-cache docstrings to describe the corrected split.
* 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>
---------
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
