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Author SHA1 Message Date
3935e300dd fix(acpx): bound Claude MCP tool calls when runtime MCP servers attach (#16360)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Hosted `claude_local` runs use the ACPX engine. Paperclip gives each
run its runtime MCP servers (for example the `paperclip-assigned` tool
gateway) as ACP `mcpServers` entries.
> - Claude's default MCP tool timeout is far longer than a run. ACP
`mcpServers` entries have no per-server timeout field. So the agent
waits on an MCP call until the call answers.
> - Hosted error reports show runs that end with "Run exceeded the
adapter execution timeout (sandbox)". The stop-time diagnostics from
#15962 show the problem: the agent went silent about 50 seconds into the
run, three tool calls of ACP kind `other` stayed pending, and nothing
ended them until the 4h sandbox backstop.
> - The gateway bounds the remote provider call (10s default, 60s max).
But other steps on the gateway `tools/call` path have no deadline: DB
queries, row locks and pool acquisition, the credential steps before the
provider timer starts, and the stdio child exit wait. One stuck step
holds the agent turn for hours.
> - This pull request gives the agent's MCP client a deadline:
`MCP_TOOL_TIMEOUT` for ACP Claude runs that receive runtime MCP servers.
> - The benefit is that a stalled gateway call becomes an MCP error that
the model can see. The turn continues and does not spend the full 4h
execution budget.

## Linked Issues or Issue Description

- Refs #15962 (diagnostics that identified the silent turn with pending
tools)
- Refs #15448, #15456, #15850 (related gateway timeout and
connection-health work; this PR does not overlap with them)

**What happened?**

A hosted `claude_local` run sent parallel MCP tool calls. No call
answered. The run stayed silent for about 4 hours. Then the sandbox
execution timeout ended it with "Run exceeded the adapter execution
timeout (sandbox)".

**Expected behavior**

A stalled MCP call ends with an error after a bounded time. The agent
sees the error and continues.

**Steps to reproduce**

1. Start an ACP `claude_local` run that has runtime MCP servers.
2. Make the gateway `tools/call` request stall (for example, hold a lock
that the request needs).
3. See that the run stays silent until the adapter execution timeout.

**Paperclip version or commit**

`master` at 976cdc7.

## What Changed

- Add `ACPX_CLAUDE_MCP_TOOL_TIMEOUT_MS` (15 minutes) in
`acpx-engine/constants.ts`. The value has wide headroom over the
gateway's longest legitimate wait (60s provider calls, 2 minutes of
approval preparation, and the 10-minute connection cap proposed in
#15850).
- The ACPX engine sets `MCP_TOOL_TIMEOUT` in the agent env for Claude
when the run has runtime MCP servers. If the adapter `env` already sets
`MCP_TOOL_TIMEOUT`, the engine keeps that value. Other agents and runs
without MCP servers do not change.
- Add an engine test for the bound, the no-server case, the user
override, and a non-Claude agent.
- Document the client-side deadline in `doc/MCP-RUNTIME-OPERATIONS.md`.

## Verification

- `npx vitest run src/acpx-engine/` in `packages/adapter-utils`: 21
files, 423 tests pass.
- The new test fails without the env assignment (`expected undefined to
be '900000'`), and passes with it.
- `npx tsc --noEmit -p packages/adapter-utils`: passes.
- The env reaches Claude through the same per-session env path as
`ANTHROPIC_MODEL`. `claude-agent-acp` merges this env into the Claude
SDK env.

## Risks

- A legitimate MCP call that takes longer than 15 minutes now fails. No
gateway path is designed to wait that long. Operators can set
`MCP_TOOL_TIMEOUT` in the adapter `env` to change the value.
- The value also applies to other MCP servers in the same Claude
session, for example servers in user settings. The same override is
available.
- Warm sessions get the env when the agent process starts again. The env
is not part of the session fingerprint, so this change does not reset
resumable sessions.
- This PR does not fix the server-side step that stalls. It bounds the
effect on the run. Server-side deadlines on the gateway `tools/call`
path (DB lock and statement timeouts, a request-level deadline, SIGKILL
escalation for stdio children) are possible follow-ups.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) through Claude Code, with tool use
and code execution. It read the repository, traced the gateway path,
edited the code, and ran the tests.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: devinfoley <devinfoley@users.noreply.github.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-14 19:01:42 -07:00
DottaandPaperclip c46e41e81c fix(heartbeat): validate native MCP gateway ownership (#14914)
## Thinking Path

> - Paperclip lets people manage agents and govern their tool access.
> - Native runs receive an immutable MCP tool assignment for one agent.
> - The gateway must enforce that owner when it authenticates a run
token.
> - Older gateway rows stored the owner only in metadata.
> - This change validates the gateway and profile, binds new rows, and
repairs valid older rows on reuse.
> - It also delivers each native assignment once.
> - Other agents cannot use the assignment, and explicit shared gateways
keep their configured scope.

## Linked Issues or Issue Description

Builds on #14012 by @busla (Jón Levy). That PR adds agent binding and
seven regressions. This PR carries that fix onto current master and adds
legacy authentication, profile validation, and duplicate-delivery
coverage. Related: #14864 improves discovery memory use.

**What happened?**
Native gateway creation stored an owner in metadata but left `agentId`
null. Authentication could therefore accept another agent's run token.
Managed discovery could also deliver historical native assignments
again.

**Expected behavior**
A native assignment accepts only its owner's run token. The gateway and
profile must refer to the same immutable assignment. The current
assignment enters the run configuration once.

**Steps to reproduce**
1. Run the database fixtures in `heartbeat-runtime-mcp-servers.test.ts`
on the baseline.
2. Create a native assignment and inspect its stored gateway owner.
3. Authenticate with another agent's run token, then inspect legacy
reuse and managed delivery.
4. The baseline fails six ownership and delivery cases. The fix passes
all twelve cases.

**Paperclip version or commit**
The red baseline is `f2e0f1963`. This PR is based on `cad26c6bf`, which
includes the merged discovery fix.

**Deployment mode**
Native Paperclip Runner execution and managed Codex MCP delivery.
Reproduction uses isolated database and HTTP fixtures.

## What Changed

- Store the agent owner and agent context on new native gateways.
- Validate profile and gateway assignment metadata before reuse or token
creation.
- Bind valid legacy rows with a company-scoped, null-owner update and
validate the result.
- Reject mismatched run tokens before legacy repair.
- Identify native assignments by gateway metadata, the reserved profile
key, or profile source. Reject missing or malformed provenance,
including JSON null.
- Exclude historical native assignments from managed gateway delivery.
Keep their rows for existing runs.
- Add twelve database and HTTP regressions and document the runtime
contract.

## Verification

- Red baseline: six regressions fail and four controls pass before the
initial fix. Two additional regressions reproduce metadata-loss
admission and a JSON-null TypeError before the review fix.
- All twelve ownership regressions pass on the final code, including
owner admission, cross-agent rejection, metadata loss, JSON-null HTTP
401, and explicit shared-gateway admission. Policy, listing-memory, and
discovery HTTP coverage also passes.
- Full workspace typecheck and build pass locally. Server typecheck and
compilation pass again after the review fix. The final ownership and
grant patches pass 42 combined database and HTTP regressions.
- [Full
CI](https://github.com/paperclipai/paperclip/actions/runs/37011383657)
passes for `626a08ae66361cf586105877e24d806b1a7a9c20`: all 54 checks
succeed; two optional Storybook checks skip. This includes full
typecheck, build, all test shards, all eight E2E shards, runner
verification, and the canary dry run.
- Greptile scores that exact head 5/5. No review threads remain
unresolved.

## Risks

Invalid historical native gateway or profile metadata now rejects
authentication. Valid unbound rows are repaired only when their owner
reuses the assignment. Conflicting owners are never overwritten.
Historical rows are retained for existing runs. Explicit shared gateways
use ordinary profiles and keep their configured scopes. The reserved
native profile namespace remains agent-owned even when gateway metadata
is cleared. No schema or dependency changes are included.

## Model Used

Original fix and seven regressions in #14012: Anthropic Claude Opus 5.5,
`claude-opus-5-5`, 1M context, as reported by @busla. Extensions and
verification: OpenAI Codex (GPT-6), with reasoning, repository
inspection, code execution, and tests. This session does not expose the
exact serving model identifier or context window.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-02 08:22:33 -05:00
Dotta 1ab159d3a7 feat(apps): consolidate connector management (#12684)
Completes the post-managed-OAuth connector lifecycle, Paperclip Cloud provisioning defaults, governed test flows, and consolidated Apps UI.\n\nCo-Authored-By: Paperclip <noreply@paperclip.ing>
2026-09-01 14:55:35 -05:00
DottaandPaperclip 3db2e6bdd2 feat(mcp) [split 8/8]: add e2e coverage and operator docs (#9563)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Governed MCP access spans contracts, runtime enforcement, adapters,
UI surfaces, and operator verification
> - The parity reference PR #9534 is too large for effective automated
or human review
> - The feature therefore needs a linear stack whose individual diffs
stay below the 100-file review limit
> - This pull request is split 8/8 and focuses on end-to-end coverage,
operator docs, evals, and release notes
> - The benefit is a standalone, testable review boundary while
preserving byte-for-byte parity at the top of the stack

## Linked Issues or Issue Description

- Related parity reference: #9534
- Problem: The complete stack needs discoverable browser scenarios,
operator guidance, threat modeling, eval coverage, and a parity proof
before merge.
- Proposed solution: Adds MCP user-story and Smoke Lab e2e suites,
docs/evals/release notes, the skill update, and the root e2e driver
script registration.
- Alternatives considered: keeping #9534 as one 403-file review, or
rewriting the feature to manufacture seams; both were rejected in favor
of path extraction plus compile-driven boundary moves.
- Roadmap alignment: this advances the existing governed MCP/tool-access
work already represented by #9534; it does not introduce a separate
roadmap initiative.
- Stack position: base branch is `pap10341-split/07-ui-apps-activation`.
- Merge policy: merge bottom-up, in order, only after the complete
eight-PR stack has been reviewed and the top-of-stack parity gate
remains empty.
- Requested review: QA for flag audit and e2e/browser acceptance;
Greptile on every PR.

## What Changed

- Adds MCP user-story and Smoke Lab e2e suites, docs/evals/release
notes, the skill update, and the root e2e driver script registration.
- Keeps this PR below 100 changed files and independently typecheckable.
- Preserves the final tree from #9534 when combined with the other seven
stack levels.

## Verification

- `pnpm typecheck`
- `node --check scripts/e2e-mcp-user-stories.mjs`
- `pnpm exec playwright test --config tests/e2e/playwright.config.ts
--list` — 43 tests discovered
- `git diff pap10341-split/08-e2e-docs
6b40e3876d9297105d4ec306e47e46d351c86172` — empty (0 bytes)

## Risks

- Browser suites depend on runtime services and environment setup; this
PR validates discovery locally while QA owns full flag-on/flag-off
execution.
- Stack risk: merging out of order can expose incomplete layers;
mitigate by following the documented bottom-up merge policy.
- Parity risk: later edits to an intermediate branch can drift from
#9534; mitigate by re-running the empty top-of-stack diff before merge.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, exact model ID `gpt-5.4`; runtime-managed context
window; medium reasoning with repository, shell, Git, GitHub CLI, and
code-execution tools enabled.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] Internal references are omitted except the execution-plan link
explicitly required for this coordinated split stack
- [x] My branch name describes the change and contains no internal
Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge


## Stack Coordination

- Internal execution plan:
[PAP-13874](/PAP/issues/PAP-13874#document-plan)
- Parity reference: #9534
- Stack: #9556 → #9557 → #9558 → #9559 → #9560 → #9561 → #9562 → #9563
- Merge bottom-up only after full-stack review and an empty parity diff
at #9563.

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-07-14 15:48:57 -05:00