Files
PaperClipAI/maps
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
..

Paperclip maps

The maps describe the same capabilities from two perspectives:

  • Feature map: what a person can do, where to reach it, and how to verify the user journey. Preserve its Poteto format.
  • Agent access map: the APIs and agent entry points for those capabilities, their permission boundaries, and access verification.

These are sibling directories under maps/. Each feature file has a same-named agent access companion. Reuse the product map's sub-feature IDs, so tasks/create identifies the same capability in both maps. Product behavior remains governed by the implementation spec; a map cannot grant authority or redefine a permission denial as success.

Access contract

Every business operation needs both an API and a usable agent entry point for an actor authorized to perform it. A dedicated tool is optional when REST, the CLI, an assigned MCP client, or native search_api / call_api already provides the operation. Record which agent surfaces actually have that path; an installed CLI or optional MCP package cannot be assumed available to every native/remote run.

Track these independently:

Dimension Values and meaning
API present, missing, not-applicable, or unreviewed. Use exact methods/paths; distinguish protocols from REST.
Agent access available, partial, missing, restricted, operator-only, not-applicable, or unreviewed. Name the supported surface and actual entry point.
Policy Actor, action/grant, company/resource/ownership scope, responsible-user intersection, run requirements, work modes, and gates relevant to the operation.
Evidence source-only, verified, failed, blocked, or not-run. Source presence and successful board calls are not agent verification.
Review depth baseline records representative operations and known gaps; operation-reviewed enumerates the capability's meaningful operations and their individual access contracts.

Broad capabilities such as task properties must be split into operations before they count as operation-reviewed: renaming, metadata edits, assignment, dependencies, and lifecycle changes can use different tools and permission rules. An available read path cannot certify a write path. List/get/create/update/delete, execution/control, credential handling, and resolution are separate where their authority or transport differs. Do not duplicate request schemas from OpenAPI.

Exceptions and restrictions

Presentation-only state, static developer fixtures, and pre-start/local operator work may use not-applicable for a domain API, with a concrete reason and the existing local path. When a capability combines shared data with presentation, split the operations: browser recents do not exempt resource lookup from API coverage. Promoting local state to a shared feature requires revisiting the entry.

A board-only endpoint is restricted for agent identity, not an automatic exception or a missing API. Cite the enforced policy and record whether the agent can request the authorized human's action and observe its result. An unresolved delegation question remains in Gaps. Company access, a job title, a personal assistant's OAuth grant, or an accepted interaction does not grant board identity. Keep budget, approval, secret and execution authority intact.

Check actual route/service authorization and production tool admission. OpenAPI actor labels and scenario/evaluation tool declarations are supporting metadata; record disagreements rather than using them as proof of access. Native API fallback restrictions, tool field/scope limits, and rollout settings are part of the agent path, even when a legacy agent can call the REST endpoint directly.

Companion file format

Each agent-access-map/<area>.md has an H1, a relative link to its product file, followed by one H2 backticked ID per product sub-feature. Each capability contains these fields:

  • Review: baseline or operation-reviewed.
  • API: presence state and exact operation IDs, or a reasoned exception.
  • Agent access: availability state and concrete entry points by surface.
  • Policy: relevant permission and runtime boundaries, with source references.
  • Evidence: evidence state, reviewed commit and sources or executed proof.
  • Verification: allowed/denied assertions and observable result; record what has actually run separately from the proposed recipe.
  • Gaps: missing APIs/paths, discovery drift, unreviewed operations or policy decisions; use none only for the enumerated scope that was reviewed.

For an operation-reviewed capability, use H3 backticked operation IDs and repeat API, Agent access, Policy, Evidence, Verification and Gaps for each operation. Use small operation names such as create, update, read, or run-now. The enclosing capability has Review: operation-reviewed only after its meaningful operations have been enumerated. The following excerpt shows one operation; include the others before using that review label:

## `definition`

Review: `operation-reviewed`.

### `create`

API: `present` — POST /api/companies/{companyId}/routines.
Agent access: `available` — agent REST, CLI routine create and native call_api
under the enabled rollout and active-run/mode gates.
Policy: same company; assigneeAgentId must be the calling agent; cite the
routine authorization and native API policy sources.
Evidence: `source-only` — reviewed commit and source links; no live proof.
Verification: `not-run` — create an owned routine; reject assignment to another
agent; inspect saved configuration, attribution and retry behavior.
Gaps: verify ownership and responsible-user resolution with a permitted agent
context; source presence alone does not qualify this operation.

Keeping the maps synchronized

When a change adds/removes a capability or changes its behavior, API, permission, tool binding, CLI support, or work mode, update the affected companion and product recipe as appropriate in the same change. Preserve IDs across renames where the capability is unchanged; update the affected cross-links together. Indexes discover recipes automatically. An API-only change may update the companion without rewriting unchanged user instructions.

maintain-verification-skill owns reconciliation of both maps. It follows changed source and authorization, checks real agent reachability, and records product gaps without implementing them during a maintenance pass. The creation skill uses this structure. verify-paperclip consumes the relevant recipes and reports evidence/drift; map editing belongs to maintenance.

Run the structural check after map changes:

node scripts/check-maps.mjs

It checks paired areas/IDs, navigation metadata, required fields, and local references. It does not certify endpoint authorization, production bindings, operation completeness, or live behavior. Source audits must check those against the existing API and tool contracts; avoid a second schema catalog or runtime.

For live access proof, use Paperclip's existing API/runner/MCP fixtures or an owned isolated instance. Use the actual agent identity, target and work mode. Assert the allowed result and relevant denial (another company/private resource, wrong owner, missing grant, invalid run, restricted mode or resolver). Mutations also need persisted state/attribution and retry behavior. Capture evidence using the existing artifact workflow; keep executed run results separate from generated maps/generated/coverage.json, which lists page references.

Local authorship and generated indexes

Change only the recipes, access contracts and stories whose behavior or intent changed. Feature recipes own navigation metadata; stories own small parameters.paperclip annotations. Do not register entries or refresh counts in shared READMEs, inventories, fingerprints or review journals.

node scripts/storybook-catalog.mjs validates and generates aggregate navigation, Storybook data, verification routes and the page inventory. All outputs live in ignored maps/generated/, ui/storybook/generated/, and the ignored Storybook preview.tsx wrapper. Start/build and UI typechecking generate their own inputs. A clean merged checkout therefore assembles both branches' changes automatically.

Git provides history and diffs. PRs, issues and CI artifacts retain review/run evidence for the named revision. Capability associations do not create whole-file review dependencies. Keep durable scenario limits in the affected recipe or story.