## Thinking Path > - Paperclip manages AI agent runs and their tool authority. > - Runner supplies provider sessions with assigned MCP connections. > - The current native connection binding supports an HTTP gateway only. > - Execution hosts also have private local tools with stdio MCP interfaces. > - Those tools need session-local registration and safe concurrency. > - This pull request adds verified local stdio assignments beside the existing gateway. > - Providers receive the existing tool schemas and image content. ## Linked Issues or Issue Description **Problem or motivation** Runner can supply a native provider session with an HTTP MCP gateway, but cannot also assign a verified local stdio MCP server without persistent provider configuration. Execution hosts need a session-local transport for local MCP tools, coordination for calls sharing a resource, and native schema/image delivery. The pinned native Codex client drops MCP images when `structuredContent` is also present. **Proposed solution** Add general stdio MCP transport support using host-assigned executable digests, arguments, environment and a private Unix socket identifying the shared resource. Tool implementations supply their own schemas and responses; Runner forwards their native MCP schemas and content. Register the transport for the current provider session. Serialize calls across processes, keep unknown outcomes fenced, and authorize assigned native Codex tools without a new prompt while routing explicit tool confirmations through existing PRP permission requests. Retain the HTTP gateway and applicable permission policy. **Alternatives considered** Reimplementing tools or translating their actions into provider-specific APIs would tie the transport to individual tool implementations. Global provider config would leak session assignments. Shell commands alone do not deliver native MCP images or preserve MCP approval requests. **Roadmap alignment** This completes the existing Runner transport boundary. Related: #10690 (operator config for the legacy ACPX engine), #11605 (gateway delivery of installed stdio connections), #16486 (preconfigured provider homes). This change assigns local tools on the execution host and leaves those administration paths intact. ## What Changed - Add reserved, verified stdio bindings for native Codex and through the shared ACPX runtime. ACPX clients must support stdio MCP assignments. Read-only sessions omit the binding. No home/project config is rewritten. - Run the backend with only its assigned environment through the verified executable launch path. - Serialize all calls sharing a private Unix socket across sessions. Metadata remains responsive. Queued cancellation prevents execution; active calls remain fenced until acknowledgement. Unknown outcomes require a resource restart. - Authorize host-assigned native Codex tools without a new per-call prompt, matching existing execution-host shell utilities. Preserve explicit tool deny/prompt rules. Route requested MCP tool confirmations through one-time PRP approvals, bound to the active thread and turn. Keep shell escalation disabled and existing tool deny rules effective. ACPX adapters retain their applicable ACPX permission policy. - Preserve schemas and image blocks. For native Codex 0.160/0.162, retain structured metadata as MCP text on image-bearing results to avoid the client's image-loss bug. ACPX adapters receive the original response. - Document transport authority, cancellation and recovery limits. ## Verification - `pnpm -r typecheck` and `pnpm build` passed with pnpm 9.15.4 and Rust 1.97.1 on macOS arm64. - Before Apex, full `paperclip-runner-core` Rust tests passed. After the fixes, all 379 library tests and eight subprocess tests using a generic stdio MCP fixture pass. Those subprocess tests cover schema/image passthrough, assigned-only environment, executable drift, call serialization, cancellation and unknown outcomes. The native Codex suite passed 91 tests with two intentionally ignored; `receipt_limit_rejects_the_call_and_keeps_polling_when_interrupt_fails` timed out waiting for `turn.interrupted`, including an isolated retry. The unchanged pre-fix commit `80917b301a2309f7966a466cf0c198a2112be2d5` reproduces the same timeout in isolation; this local native-suite run is not claimed as fully passing. - All 252 native controller tests pass against the final narrowed approval branch. Focused TypeScript transport/permission suites passed (298 tests); final binding, read-only host, policy and adapter checks passed (105 tests). - **Provider-client smoke coverage:** pinned Codex 0.160.0 through native Runner and Claude SDK 0.3.286 used local stdio MCP servers and loopback model API fixtures without live model credentials. These clients define the smoke-test coverage; this is not an exhaustive adapter compatibility test. Image responses reached the next model request as typed image blocks. Native Codex checks also verified unattended execution without approval requests, explicit per-tool prompt denial without backend execution, disabled-tool rules, and stale-turn approval rejection. - Two Greptile concurrency findings were reproduced with failing subprocess tests and fixed: pending cancellation under output backpressure, and a ctime-based fence reset after chmod. Initial checks exposed Codex CLI option-scope and key-quoting errors, which were corrected. The existing ordinary elicitation regression also exposed an overly broad request branch; the final branch handles explicit tool approvals only. - `pnpm test:run` was attempted. The broad local server suite hit persistent embedded PostgreSQL startup failures and unrelated local Git fixture failures; it was stopped with the failure log retained. Those local results are not claimed as passing. Hosted Linux CI gates passed on the reviewed runtime commit, as recorded below. - First Apex review found three additional defects, now fixed with regressions: keep the resource-lock socket snapshot instead of sampling the socket twice; project native permission requests with durable turn/item IDs while retaining provider IDs in details; validate provider response conversion before marking a request as settling. The retry regression failed before the fix. Focused Codex request/adapter checks pass (23 tests), server permission projection passes (16 tests), and all 379 Runner library tests pass. The broader database-backed bridge suite was attempted but its local PostgreSQL setup timed out; 29 tests did not execute. This local failure is retained, not claimed as passing. - Runtime acceptance before the documentation clarification, on `bd4fccae001157beb5bc76ff17c1920a5db3105a`: standard Greptile 5/5, then Apex 5/5 with no unresolved threads; all 60 checks complete successfully or intentionally skip. Ten CI jobs were interrupted by the same runner shutdown, including one stale job that required cancellation before retry; the same-commit retry passed. Hosted Rust tests also pass, including the native suite with the local baseline timeout noted above. - `git diff --check`, map validation, and pre-push secret/PII scan passed. ## Risks - No live model account or deployment isolation qualification was run. The loopback fixture proves the actual vendor-client request format, not model interpretation. - Stdio MCP support uses the current host-assignment contract: each binding requires a verified executable and a private Unix socket identifying the serialized resource. Other platforms retain the HTTP path. No provider version was upgraded. - A lost acknowledgement blocks subsequent calls until the host restarts the assigned resource. Direct shell calls are outside this MCP fence and retain the existing shell policy. - Preconfigured Claude remains unattended and denies interactive approval requests. Host assignment authorizes native Codex local tools; it must be supplied only for sessions already authorized to use the resource. ## Model Used OpenAI Codex, GPT-6, with reasoning and repository/tool execution. The session does not expose a more specific model identifier or context-window size. ## 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 - [ ] 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 --------- Co-authored-by: Paperclip <noreply@paperclip.ing>
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:
baselineoroperation-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
noneonly 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.