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PaperClipAI/maps/agent-access-map/gateways-profiles.md
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DottaandPaperclip 1e731520bb fix(mcp): deduplicate discovered tool descriptors (#16281)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents receive governed app tools through the MCP gateway.
> - GitHub review tasks can contain a PR discussion and inline finding
threads.
> - Discovery repeated each tool for every conversation linked to the
task.
> - Native tool registration treated these repeated descriptors as a
fatal collision.
> - This pull request lists GitHub tools once and deduplicates identical
descriptors across providers.
> - Agents can continue work while conflicting definitions and normal
tool permissions remain enforced.

## Linked Issues or Issue Description

**What happened?**

A follow-up run on a GitHub review task failed with
`assigned_mcp_tool_name_collision` before the provider started. The task
had a main conversation and an inline finding thread. Discovery returned
the same seven tools twice. Repeated descriptors from other providers
could cause the same failure.

**Expected behavior**

Discovery exposes each identical tool once. Separate connection names
remain separate tools. Conflicting definitions remain an error. Every
call still passes the gateway's policy, approval, revocation, and audit
checks.

**Steps to reproduce**

1. Run a GitHub review and publish an inline finding.
2. Send a follow-up request on the same PR task.
3. Inspect the task-bound bot catalog and the next native startup.
4. Separately, return two identical descriptors from an assigned app or
plugin catalog.

Related: #13717 added the GitHub review workflow.

## What Changed

- Use a distinct GitHub discovery query across conversations that share
an endpoint and task. Keep both thread mappings.
- Deduplicate identical gateway descriptors by their full gateway name
across providers. Use this rule for MCP listings, plugin listings,
assigned-tool startup, and fresh assigned-tool discovery.
- Reject conflicting descriptors with `tool_name_collision`. Keep the
projected-name collision guard.
- Cover GitHub inline-thread discovery, repeated plugin/app tools,
direct and on-demand catalogs, revocation, conflicting bindings, and
separate connection names.
- Update the execution contract, GitHub documentation, and agent access
map.

## Verification

- Regression baseline: six new assertions failed on the original
implementation. GitHub returned fourteen entries, plugin discovery
repeated a tool, and native startup failed on repeated app tools.
- Focused verification passed: 272 GitHub cases, all 29 assigned-tool
cases, and all 88 gateway acceptance cases.
- `pnpm -r typecheck` passed.
- `pnpm build` passed.
- `node scripts/check-maps.mjs` passed.
- Current-head CI passed: 55 checks passed, two inapplicable checks
skipped. Greptile scored the current head 5/5 with no unresolved
threads.
- Full local `pnpm test:run` encountered a 15-second timeout in the
existing bearer-auth throttling test, before tool discovery. That test
passed in the separate 88-case gateway run and on one isolated rerun.
The duplicate broad local run was then stopped; the complete
current-head CI matrix passed.

## Risks

- Deduplication keeps the first identical descriptor and preserves
listing order. Same-name descriptors with different definitions fail
with HTTP 409 rather than selecting an ambiguous binding.
- The GitHub query changes result cardinality. It retains the existing
task/company/agent filters and leaves conversation rows intact.
- No schema migration or credential change. Live staging recovery
requires deployment and a new authorized run.

## Model Used

OpenAI Codex, based on GPT-6, with code inspection, editing, browser
investigation, and test execution. The exact serving model ID and
context window are not exposed in this session.

## 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>
2026-10-14 07:39:54 -05:00

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Markdown

# Tool gateways and access profiles — agent access
Product map: [Tool gateways and access profiles](../feature-map/gateways-profiles.md).
Review date: 2026-10-12. Source commit: `58e16dbddfc9c8d0cf60867f9d9847f0feda055b`.
Native REST transport reconciled in this change; see the
[shared transport contract](README.md#native-rest-transport).
This is a source-reviewed baseline of representative operations and known gaps.
Each capability needs operation-level review before its entire scope can be
qualified. No live agent execution is claimed. Follow the [map contract](../README.md)
for format, permission checks, evidence and maintenance.
## `gateway`
Review: `baseline`.
API: `present` — representative operation IDs:
- `POST /api/companies/{companyId}/tools/gateways`.
Agent access: `restricted` — Board tools:admin REST; CLI connections/configuration where
supported.
Policy: Named gateway/profile administration and credentials are board tools:admin;
agent sessions/tool use use separate scoped authority.
Evidence: `source-only` — [implementation](../../server/src/routes/tool-gateway.ts#L353)
at the reviewed commit above.
Verification: `not-run` — assert the documented agent denial with an owned test fixture;
verify any listed agent request/result path separately. A delegated operation needs its
own policy and access review.
Gaps: No agent named-gateway management path; assigned tool use exists separately.
## `profiles`
Review: `baseline`.
API: `present` — representative operation IDs:
- `POST /api/companies/{companyId}/tools/profiles`.
- `PATCH /api/tool-profiles/{profileId}`.
Agent access: `restricted` — Board management REST; agent receives effective tool
assignment.
Policy: Named gateway/profile administration and credentials are board tools:admin;
agent sessions/tool use use separate scoped authority.
Evidence: `source-only` — [implementation](../../server/src/routes/tool-gateway.ts#L353)
at the reviewed commit above.
Verification: `not-run` — assert the documented agent denial with an owned test fixture;
verify any listed agent request/result path separately. A delegated operation needs its
own policy and access review.
Gaps: Agent access to tools does not permit profile editing.
## `client-connect`
Review: `baseline`.
API: `present` — representative operation IDs:
- `GET /api/tool-gateway/gateways/{gatewayId}/mcp`.
- `POST /api/tool-gateway/sessions`.
Agent access: `partial` — Agent REST / native `call_api` for scoped session creation
and revocation; existing MCP client protocol and assigned native app tools.
Policy: Named gateway/profile administration and credentials are board tools:admin;
agent sessions/tool use use separate scoped authority.
Evidence: `source-only` — [implementation](../../server/src/routes/tool-gateway.ts#L353)
at the reviewed commit above.
Verification: `not-run` — exercise a listed permitted operation with actual agent
credentials/run context; inspect its result and applicable persistence/attribution.
Assert the relevant denied actor, owner, company or mode from Policy. Review the
remaining operations before qualifying the whole capability.
Gaps: Scoped sessions remain agent/run-bound. MCP requires its existing protocol
client; named gateways and gateway-token management retain board permissions.
Discovery collapses identical descriptors with the same gateway name across
providers, including native assigned-tool startup and fresh searches. Conflicting
definitions remain an error. Distinct names and the normal invocation grants,
approvals and revocation checks remain independent. Regression coverage lives in
[gateway tests](../../server/src/__tests__/tool-gateway.test.ts) and
[assigned-tool tests](../../server/src/services/native-runtime/assigned-mcp-tools.test.ts);
these fixtures do not certify a live external-client journey.
## `tokens`
Review: `baseline`.
API: `present` — representative operation IDs:
- `POST /api/tool-gateway/gateways/{gatewayId}/tokens`.
- `POST /api/tool-gateway/gateway-tokens/{tokenId}/revoke`.
Agent access: `restricted` — Board tools:admin token management.
Policy: Named gateway/profile administration and credentials are board tools:admin;
agent sessions/tool use use separate scoped authority.
Evidence: `source-only` — [implementation](../../server/src/routes/tool-gateway.ts#L353)
at the reviewed commit above.
Verification: `not-run` — assert the documented agent denial with an owned test fixture;
verify any listed agent request/result path separately. A delegated operation needs its
own policy and access review.
Gaps: Gateway-token management requires board tools:admin at the HTTP route.
A grant to use an app does not create this authority; native `call_api` preserves
the denial.
## `activity`
Review: `baseline`.
API: `present` — representative operation IDs:
- `GET /api/tool-gateway/audit`.
Agent access: `restricted` — Board tools:view_audit; agent receives its own tool
receipts/errors.
Policy: Named gateway/profile administration and credentials are board tools:admin;
agent sessions/tool use use separate scoped authority.
Evidence: `source-only` — [implementation](../../server/src/routes/tool-gateway.ts#L353)
at the reviewed commit above.
Verification: `not-run` — assert the documented agent denial with an owned test fixture;
verify any listed agent request/result path separately. A delegated operation needs its
own policy and access review.
Gaps: Audit management API exists but broad audit visibility is not an agent use-path
guarantee.