## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The runner package is useful only when the application can start,
observe, and recover a native Codex run safely.
> - Existing direct adapters must keep their current execution and
finalization paths.
> - The application boundary therefore needs additive persistence,
authorization, coordination, and recovery behind an explicit
experimental adapter.
> - This pull request adds that Codex-only boundary without activating
generalized providers, remote environments, or the later task/SDK
surfaces.
## Linked Issues or Issue Description
**Subsystem affected**
Shared contracts, database persistence, adapter utilities, server
native-runtime services, and the experimental Paperclip Runner adapter.
**Problem or motivation**
The already-landed runner package has a qualified Codex path, but the
application needs durable native-run state, guarded runtime selection,
authenticated coordination, tool security, finalization, and recovery
before the experimental adapter can be exercised safely.
**Proposed solution**
Add a Codex-only `paperclip_runner` application path behind the existing
default-off native-runner setting. Bind native state and coordination to
company/run identity, preserve persisted-run recovery, and leave every
direct adapter on its existing legacy execution path.
**Alternatives considered**
The earlier stack boundary introduced a generalized executor and
remote-environment lifecycle here. That made this PR depend on
implementations in higher PRs and changed reusable sandbox behavior
globally. Those pieces are now deferred together to #12592.
**Roadmap alignment**
ROADMAP.md does not list a conflicting native-runner integration
project. This change adds the application boundary for the existing
Runner architecture.
## What Changed
- Added native run/result/finalization/provider-trace persistence,
shared validators, and idempotent migration/replay coverage.
- Added guarded Codex-only runtime selection, authenticated PRP
coordination, recovery, finalization, and interaction services.
- Added run/company-bound tool-gateway authorization, credential
redaction, SSRF protections, and replay-safe behavior.
- Added the explicit `paperclip_runner` adapter behind the default-off
rollout setting.
- Preserved legacy answered-question wake projection and direct-adapter
execution/finalization paths.
- Hardened cancellation so only owned in-memory child processes are
signaled; persisted recycled PIDs/process groups are never trusted.
- Retained the narrow Claude ACPX isolated-context security follow-up
discovered after #12590.
- Deferred the generalized executor, provider ingress, remote lifecycle,
SDK/lab/eval work, release-process changes, and lockfile.
## Verification
- Changed-file delta against `master`: 133 files.
- GitHub Actions is the authoritative verification environment for this
PR.
- Full CI, security, and Greptile review will run on this lowest
unmerged stack PR.
- Local tests/build/typecheck were not run because this checkout is
resource constrained.
- Static diff/reference checks pass, and `pnpm-lock.yaml` is unchanged.
## Risks
- This touches central heartbeat and agent-route code, so legacy
compatibility is the primary risk.
- Runtime selection remains Codex-only and explicit; direct Codex,
Claude, OpenCode, process, HTTP, and plugin adapters remain on their
existing paths.
- Fresh native starts fail closed while the rollout flag is off;
persisted native records remain readable and recoverable.
- Cancellation, company/run binding, tool calls, status decisions, and
completion writes are guarded or replay-safe.
> 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.
## Model Used
OpenAI Codex, GPT-5.6, with repository tools, code execution, and
parallel agent review.
## 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 linked existing issues or described the issue in-PR
following the relevant issue template
- [x] I have not referenced internal or instance-local Paperclip issues
or links
- [x] My branch name describes the change and contains no internal
Paperclip ticket id
- [ ] I have run tests locally and they pass — GitHub Actions is
authoritative for this resource-constrained checkout
- [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 risks above
- [ ] All Paperclip CI and security gates are green
- [ ] Greptile is 5/5 with no open actionable findings
- [x] I will address all Greptile and reviewer comments before merge
## Stack
- Position: 3 of 5 overall; lowest of 3 currently unmerged
- Base: `master`
- Previous:
[#12590](https://github.com/paperclipai/paperclip/pull/12590), qualified
Claude ACPX runtime — merged
- Next: [#12592](https://github.com/paperclipai/paperclip/pull/12592),
generalized Codex executor, task experience, and developer SDKs
---------
Co-authored-by: Dev Agent <dev@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents need a governed way to request app connections during issue
work.
> - The catalog now describes the available providers and setup methods.
> - A request must become a durable, company-scoped intent before an
operator acts on it.
> - This pull request adds that intent runtime across server, agent,
CLI, and shared contracts.
> - The benefit is a safe bridge from agent need to operator-approved
setup.
## Linked Issues or Issue Description
Refs #11965
This is stack 7 of 11. It depends on stack 6 and replaces another
reviewable part of #11965.
## What Changed
- Add connection intent types, validation, service logic, and routes.
- Add agent runtime tools and CLI support for connection requests.
- Add issue-thread interaction support for connection intents.
- Add runtime, route, adapter, and contract tests.
- Hold the final resolved-continuation row lock through asynchronous
adapter preparation until an actual process spawn, so parking or
reassignment cannot cross that boundary.
- Report Hermes Gateway's first remote run request through the shared
dispatch hook so the resolved-intent lock is released at the true
dispatch boundary.
- Revalidate the addressed user's live non-viewer membership and
connection-management authority for every intent mutation, including
OAuth completion.
## Verification
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/tool-access-service.test.ts`
- Result: 176 tests passed.
- `pnpm build`
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-stale-queue-invalidation.test.ts` (32 passed;
includes non-process dispatch lock-release coverage)
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/connection-intents-service.test.ts -t
"addressed-user mutation"` (1 passed)
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/tool-access-service.test.ts -t "binds OAuth
callback completion to the initiating board session"` (1 passed)
- `pnpm --filter @paperclipai/hermes-paperclip-adapter test --
src/gateway/server/execute.test.ts` (23 passed; includes dispatch-hook
ordering and exactly-once coverage)
- `pnpm --filter @paperclipai/hermes-paperclip-adapter typecheck`
## Risks
- A malformed intent could create an unusable operator request.
- Validators and company checks reject invalid or cross-company
requests.
- The final continuation gate holds the issue row lock through adapter
preparation until process or remote dispatch; later operator changes use
the normal active-run interruption path.
- The change does not add a database migration.
> I checked `ROADMAP.md`. This stack continues the existing app
connection work from #11965 and does not duplicate another planned item.
## Model Used
OpenAI Codex, GPT-5. The runtime model ID and context window were not
exposed. The model used reasoning, tool use, and code execution.
## 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 linked the public source pull request with `Refs #`
- [x] I have not referenced internal or instance-local Paperclip issues
or links
- [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
- [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>
## Thinking Path
> - Paperclip is the open source control plane people use to organize
and operate AI-agent companies.
> - Agent behavior depends partly on the bundled Paperclip core skill
synchronized into each runtime.
> - The existing database and runtime plumbing already supports
immutable skill-version snapshots and per-agent version selections, but
no product workflow exposed that capability.
> - Replacing the live bundled skill globally would make champion
adoption risky and difficult to compare across agents.
> - This pull request adds an experimental, instance-level beta-skills
gate plus a repository release registry, immutable seeded releases,
enforcement, and a per-agent release picker.
> - The benefit is controlled per-agent evaluation of frozen core-skill
releases while the default-off path remains behaviorally unchanged.
## Linked Issues or Issue Description
### Subsystem affected
Cross-cutting: `server/`, `ui/`, `packages/db`, and `packages/shared`.
### Problem or motivation
Paperclip needs a safe way to evaluate improved versions of its core
operating skill without globally replacing the live default. Today the
version-snapshot and per-agent pin plumbing exists, but operators cannot
use it. A global replacement would make regressions difficult to contain
and would prevent controlled comparisons across agents.
### Proposed solution
Add a default-off instance experiment that exposes immutable, named
core-skill releases. When enabled, operators can pin each agent to a
seeded release; when disabled, every agent resolves the live default
while saved pins remain intact. Validate pinned writes at the API
boundary, gate reads at runtime, and expose the selection in the agent
Skills tab.
### Alternatives considered
- **Replace the bundled core skill globally:** rejected because it
changes every agent at once and provides no rollback/isolation boundary.
- **Ship releases as separate skills:** rejected because releases are
versions of one core capability, not independently enabled skills.
- **Store release snapshots only outside the repository:** rejected
because repository provenance and hashes make builds reproducible and
reviewable.
### Roadmap alignment
This extends the Skills Manager / Skill Studio direction in `ROADMAP.md`
by making core-skill versions operable per agent. It does not duplicate
another open implementation PR; GitHub searches found no related
`enableBetaSkills` change.
### Additional context
The feature remains experimental and default off. The V7 champion was
selected through a multi-model evaluation process, and the frozen
release contents are verified by SHA-256 below.
## What Changed
- Added the default-off instance-level `enableBetaSkills` experimental
flag.
- Added `skills-releases/paperclip/` with the ordered release registry
and frozen `v0` plus `v7-roster` snapshots.
- Added release metadata to `company_skill_versions` and idempotent
release seeding. The migration was planned as `0191`, then renumbered to
`0192` because current `master` claimed `0191` before final rebase.
- Added read-time gating and write-time validation so disabled instances
always resolve the live default and reject pinned-version writes.
- Added the per-agent Release picker in the agent Skills tab, including
responsive layout and beta-pin state.
- Kept `EDITS.md` out of the release registry and PR diff.
### V7 Adoption Evidence
- Paid roster: 6 models, 94-case suite.
- Result: 553/564 pass-within-2, mean 92.17/94, versus the P2 baseline
of 544/564.
- Reference model improved 84→91; maximin improved 84→90.
- Final report:
https://pages.paperclip.ing/skills/optimization/paperclip/pap-14624-p3-final-20260721/
### Provenance
- `v7-roster` is the Phase 1 champion plus additions-only edits
E107–E112. Per-edit rationale remains in the evals repository at
`source/v7-roster/EDITS.md` and is deliberately excluded from this PR.
- `v0` is the `skills/paperclip` tree from commit `ea66ea81`.
- Champion selection was accepted on July 21, 2026 via board card
`9c304fc2` (PAP-14624 G3).
- This delivery mechanism was accepted on July 24, 2026 via plan
revision `2367abd2` (PAP-14858).
### QA Evidence
- P4 QA matrix comment `b7f40522-4e9b-4a3a-9821-28e86fe1a987`: all 6
acceptance criteria passed.
- Automated QA matrix: 166 tests passed with 0 failures, including real
filesystem materialization and full SHA-256 assertions.
- UI QA exercised the real agent Skills tab at desktop and mobile widths
with the experimental flag both on and off.
## Verification
- `pnpm check:token-gates`
- Focused beta-release matrix: 169 tests passed across shared
validators, server services/routes/heartbeat behavior, instance settings
UI, and release picker UI.
- `pnpm -r typecheck`
- `pnpm build`
- `pnpm test:run`: server and UI partitions passed; one CLI doctor test
inherited temporary AWS credentials from the agent heartbeat and
expected no static credentials. The isolated rerun with
`AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, and `AWS_SESSION_TOKEN`
unset passed 8/8.
- V7 SHA-256:
- `SKILL.md`:
`53ab290489684cbf116fdd1406a95f6b6f53c9c36358b1bf8bfeae481e253575`
- `references/cases.md`:
`3b821f59064a7761091020a14819a8d787131f24029748563d6c0e1be7e6eaec`
- `references/workflows.md`:
`69747bd6e05f7e3673d1e67b07ff295df1869c05e1fd029804d5fa9177db92cd`
- Confirmed 49 changed files, no `pnpm-lock.yaml`, no workflow changes,
and no `EDITS.md`.
## Risks
- **Migration:** low-to-moderate risk. Three nullable columns and one
partial unique index are added idempotently; existing rows remain valid.
- **Behavior:** low risk while the flag is off because read-time
resolution forces the live default and saved pins are preserved but
inactive.
- **Frozen content:** release snapshots intentionally diverge from
future live skill edits; provenance and hashes make that divergence
explicit and reproducible.
- **UI:** low risk. The picker only renders for the bundled core skill
when the experimental flag is enabled and seeded releases exist.
> This extends the existing Skills Manager / Skill Studio direction
described in `ROADMAP.md`; it does not duplicate another open
implementation PR. The GitHub PR search found no related
`enableBetaSkills` change.
## Model Used
- OpenAI Codex using `gpt-5.5` with reasoning and
terminal/code-execution tools; context-window size is not exposed by
this runtime. Earlier implementation commits also record Claude Opus 4.8
assistance where applicable.
## 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
- [ ] I have not referenced internal/instance-local Paperclip issues or
links (required governance identifiers are included above; no internal
URL is included)
- [ ] My branch name describes the change and contains no internal
Paperclip ticket id (the approved delivery plan mandated this shared
branch name)
- [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>
## Thinking Path
> - Paperclip is the open source control plane people use to manage
AI-agent companies and their governed access to external systems.
> - Connected Apps build on the existing Apps and MCP gateway substrate
so companies can configure reusable, auditable integrations.
> - The current connection record does not yet have a stable public
address, explicit ownership/auth method fields, or subject-specific
credential grants.
> - Without that schema core, later OAuth, per-user authorization, token
brokering, triggers, and connector-service phases cannot enforce tenant
and subject boundaries consistently.
> - This pull request adds the forward-compatible Connections v3 schema
core while preserving the existing connection lifecycle and directly
migrating the remote MCP transport name.
> - The benefit is a company-scoped, least-privilege foundation for
one-click integrations without bypassing Paperclip secrets, profiles,
rules, or audit controls.
## Linked Issues or Issue Description
No matching public issue was found.
**Problem**
Paperclip's current app connections need a durable identity and
authorization substrate before Connected Apps can safely support
multiple setup methods, per-user credentials, provider tenants, and
managed connector services. The existing schema only models a single
connection-level credential set and uses legacy transport terminology.
**Proposed solution**
Add a stable company-scoped connection UID, explicit
ownership/auth/transport fields, a subject-aware `connection_grants`
table, and multi-key credential annotations. Backfill existing
connections and workspace grants in a reversible migration, then update
shared/server/UI contracts to the new `mcp_remote` transport name.
**Related work**
- Related foundation: #9534
- Roadmap: Connected Apps (one-click integrations)
## What Changed
- Added company-scoped connection `uid`, `ownership`, `authKind`, and
canonical transport fields across database, shared contracts,
validators, services, and UI fixtures.
- Added `connection_grants` with workspace/user subject rules, provider
tenant metadata, credential secret refs, revocation state, company
scoping, and uniqueness constraints.
- Added migration `0182_connections_v3_schema_core` to backfill stable
UIDs, rename `remote_http` to `mcp_remote`, infer auth kinds, create
default workspace grants, and support rollback coverage.
- Added multi-key credential annotations and updated gateway/access
services without changing the existing lifecycle behavior.
- Updated the connection glossary, connector playbook, and security
threat model for the new identity, grant, and relay boundaries.
- Added explicit test UIDs to direct database fixtures so the new
non-null invariant is exercised across affected server suites.
## Verification
- `pnpm --filter @paperclipai/shared typecheck`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck`
- `pnpm exec vitest run server/src/__tests__/tool-access-service.test.ts
server/src/__tests__/tool-gateway-service.test.ts
server/src/__tests__/tool-gateway.test.ts
server/src/__tests__/heartbeat-runtime-skills.test.ts
server/src/__tests__/tool-oauth-legacy-backfill.test.ts
server/src/__tests__/tool-access-policy-service.test.ts
server/src/__tests__/heartbeat-runtime-mcp-servers.test.ts
packages/db/src/connections-v3-schema-core-migration.test.ts
packages/shared/src/validators/tool-access.test.ts --config
vitest.config.ts` — 9 files, 218 tests passed.
- Latest-head GitHub Actions: build, typecheck, general/serialized
suites, backup/worktree restore coverage, both e2e shards, canary,
policy, and security scans pass.
- Greptile: 5/5 with zero unresolved threads.
- `pnpm check:token-gates` remains red only on five pre-existing `#9627`
color literals outside this change.
## Risks
- **Migration risk:** UID backfill and default-grant creation touch
every existing connection. The migration uses company-scoped uniqueness,
deterministic legacy UIDs with ID suffixes, and seeded up/rollback
coverage.
- **Authorization risk:** Grant rows carry credential references.
Constraints enforce workspace-vs-user subject shape, company/connection
lookup indexes, one default grant per connection, and one user grant per
connection/subject. Security review is requested specifically for this
design.
- **Compatibility risk:** `remote_http` is renamed directly to
`mcp_remote`; all repository call sites and fixtures are updated in the
same change.
- **Future-phase risk:** Subject-bound token issuance, triggers, and
connector-service relay verification remain fail-closed requirements
documented for later phases; this PR does not expose those capabilities.
> 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 CLI coding agent. The runtime did not expose an exact
underlying model ID or context-window size; capabilities used include
repository inspection, code editing, shell execution, test execution,
Git/GitHub CLI operations, and structured reasoning.
## 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>
## 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 4/8 and focuses on gateway runtime, Smoke
Lab, plugins, and server wiring
> - 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 policy core needs runtime execution, endpoint guards,
route registration, heartbeat integration, and adapter MCP injection to
become operational.
- Proposed solution: Adds the remaining server routes/wiring/consumers,
runtime tests, adapter-utils MCP contracts, and Claude/Codex injection
implementations required by the server layer.
- 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/03-server-tool-access`.
- 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: SecurityEngineer for gateway, endpoint guard, token
issuance, and runtime wiring; Greptile on every PR.
## What Changed
- Adds the remaining server routes/wiring/consumers, runtime tests,
adapter-utils MCP contracts, and Claude/Codex injection implementations
required by the server layer.
- 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`
- Changed server test set — 26 files, 382 tests passed
- Affected server adapter tests — 38 tests passed after concrete adapter
boundary move
- Adapter-utils and Codex focused tests — 76 tests passed
## Risks
- Remote endpoint validation, token handling, and runtime supervision
are security-sensitive and can fail closed or deny legitimate access if
misconfigured.
- 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agent runs often need provider credentials, API tokens, and other
environment-bound secrets.
> - Company-level secrets work for shared credentials, but they do not
model values that should differ by human operator.
> - Without a user-scoped model, a run can dispatch without knowing
whether the responsible human has supplied the needed value.
> - Paperclip also needs run attribution to make those user-scoped
runtime checks deterministic and auditable.
> - This pull request adds user-specific secret definitions, per-user
values, environment bindings, responsible-user attribution, and runtime
resolution gates.
> - The benefit is that teams can define the secret once, let each user
provide their own value, and block runs before dispatch when required
user secrets or active definitions are unavailable.
## Linked Issues or Issue Description
Refs #224
Refs #6057
This PR implements user-specific secret support as a core
secret-management capability rather than a one-off adapter setting. It
is related to existing public work on company secrets UI and runtime
secret refs, but is distinct because the value is owned by the
responsible user and resolved at run dispatch time.
Related PR search before opening found existing secrets work such as
#1550, #8256, #8614, #8634, and #8647; none of those add the full
user-secret definition/value/runtime gate covered here.
## What Changed
- Added user-secret definitions and per-user "My secrets" values,
keeping stored values out of access metadata.
- Added `user_secret_ref` environment bindings and UI affordances to
pick them alongside existing secret refs.
- Added responsible-user runtime resolution so user-secret refs resolve
against the human responsible for the run.
- Added pre-dispatch missing-secret gates so runs fail before adapter
dispatch when required user values are absent or definitions are
inactive.
- Added low-trust allowlist hardening for user-secret runtime access.
- Added issue, routine, run, and agent API key responsible-user
attribution and fail-closed dispatch behavior when attribution cannot be
resolved.
- Added denial-copy mapping so responsible-user authorization failures
surface as actionable run outcomes instead of opaque setup failures.
- Added OpenAPI documentation for the user-secret routes.
- Rebases cleanly on current `master`; migrations were renumbered
incrementally as `0128_user_specific_secrets`,
`0129_agent_api_key_responsible_user`, and
`0130_run_responsible_user_invariant` after upstream `0126`/`0127`
migrations.
- Removed previously committed local design screenshots so the PR
contains code/docs/tests only.
## Verification
- PASS: PR head `2527febd106bcf3ca264ca0da7fca491084192d6` is based on
`paperclipai/paperclip:master`.
- PASS: `git diff --check`
- PASS: `git diff --name-only public/master...HEAD | rg
'^(pnpm-lock\\.yaml|\\.github/workflows/|screenshots/)' || true`
produced no files.
- PASS: migration journal audit confirmed unique indexes through `130`
with tail entries `0126_issue_comment_derived_attribution`,
`0127_environment_custom_images_instance_scoped`,
`0128_user_specific_secrets`, `0129_agent_api_key_responsible_user`, and
`0130_run_responsible_user_invariant`.
- PASS: `pnpm --filter @paperclipai/ui typecheck`
- PASS: `pnpm --filter @paperclipai/server typecheck`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-responsible-user-invariant.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-active-run-output-watchdog.test.ts
src/__tests__/heartbeat-stale-queue-invalidation.test.ts
src/__tests__/heartbeat-workspace-finalize-branch.test.ts
src/__tests__/issue-monitor-scheduler.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-comment-wake-batching.test.ts
src/__tests__/heartbeat-retry-scheduling.test.ts
src/__tests__/heartbeat-accepted-plan-workspace-refresh.test.ts
src/__tests__/heartbeat-plugin-environment.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/low-trust-red-team-routes.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/secrets-service.test.ts` (55 tests)
- PASS: `pnpm vitest run server/src/__tests__/secrets-routes.test.ts
server/src/__tests__/secrets-service.test.ts` (89 tests after final
Greptile cleanup fixes)
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-issue-liveness-escalation.test.ts` (17 tests
after the final rebase CI fix)
- PASS: focused server Vitest batches covering heartbeat recovery,
project env, plugin env, routines, low-trust, pipelines, monitors,
watchdog, and stale queue paths.
- PASS: GitHub checks are green on
`2527febd106bcf3ca264ca0da7fca491084192d6`, including Typecheck +
Release Registry, Build, General tests, serialized server suites, e2e,
Canary Dry Run, verify, security checks, and Greptile Review.
- PASS: Greptile Review completed successfully on
`2527febd106bcf3ca264ca0da7fca491084192d6` with Confidence Score 5/5,
and GraphQL review-thread audit returned zero unresolved non-outdated
threads.
## Risks
- Runtime behavior now depends on a run having a correct responsible
user; missing or incorrect responsibility assignment can block runs
before adapter dispatch.
- `user_secret_ref` bindings intentionally expose metadata without
values, but UI/API callers may need to handle the new binding kind
explicitly.
- External secret providers and IAM policies are not automatically
provisioned by this PR; operators still need to configure provider-side
access for non-local vaults.
- The PR is broad across db/shared/server/UI/runtime paths, so release
validation should include both API and UI secret workflows before merge.
- The migration renumbering is intentionally incremental after upstream
migrations; the branch migrations use guarded
column/table/index/constraint creation so users who tested the older
draft numbering should not hit duplicate DDL for the existing objects.
> 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, GPT-5-based coding agent (`gpt-5`), Codex local adapter
with shell/tool use and code execution. Context window and internal
reasoning mode are not exposed by the runtime.
## 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>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents increasingly depend on reusable skills, so the control plane
needs a first-class way to browse, inspect, install, version, and attach
those skills.
> - The old skills surface was mostly operational plumbing; it did not
give operators a store-like discovery flow, canonical detail URLs, rich
source/version context, or creation paths.
> - The backend also needed stronger contracts around company skill
metadata, versions, install counts, runtime materialization, and adapter
skill preferences.
> - This pull request builds the Skills Store foundation across DB,
shared contracts, server routes/services, UI, and Storybook.
> - The benefit is a more inspectable, operator-friendly skill workflow
that still preserves company-scoped control-plane boundaries and agent
runtime behavior.
## Linked Issues or Issue Description
No GitHub issue exists for this Paperclip work item. Paperclip task
refs: PAP-10846 and PAP-10921.
Feature request:
Paperclip operators need a single Skills Store experience where company
skills can be discovered, inspected, created, versioned, installed, and
attached to agents without relying on scattered operational screens or
implicit runtime state.
Related PR search:
- Searched GitHub for `Skills Store`, `company skills`, and `skill
detail`.
- Found several open skills-related PRs such as #7809 and #4409, but no
duplicate PR for this end-to-end Skills Store branch.
## What Changed
- Added the Skills Store backend foundation: company skill schema
fields, migrations, shared types/validators, and expanded server skill
routes/services.
- Added skill discovery, category navigation, canonical skill detail
routes, tabs, source attribution, version snapshots/diffs, install count
backfill, and creation flows.
- Updated agent skill preference handling so version selections survive
runtime mention injection and runtime skill materialization honors
pinned versions.
- Preserved unversioned skill assignments as live/current selections
instead of silently pinning them to the current version at assignment
time.
- Added focused regression coverage for company skill routes/services,
route helpers, UI behavior, skill version diffs, and runtime skill
version pins.
- Added Storybook coverage for Skills Store discovery/detail states and
updated the main layout navigation.
- Addressed Greptile findings around version creation races,
soft-deleted comments, fork metadata scoping, GitHub skill directory
fallback, runtime snapshot materialization, shared runtime
skill-selection helpers, and version-assignment semantics.
## Verification
- `pnpm exec vitest run
server/src/__tests__/heartbeat-project-env.test.ts
server/src/__tests__/heartbeat-runtime-skills.test.ts`
- `pnpm exec vitest run
packages/shared/src/validators/company-skill.test.ts`
- `pnpm exec vitest run server/src/__tests__/company-portability.test.ts
server/src/__tests__/company-skills-service.test.ts`
- `pnpm exec vitest run
cli/src/__tests__/company-import-export-e2e.test.ts`
- `pnpm exec vitest run
server/src/__tests__/agent-skills-routes.test.ts`
- `pnpm exec vitest run server/src/__tests__/openapi-routes.test.ts`
- `pnpm exec vitest run
server/src/__tests__/company-skills-service.test.ts
server/src/__tests__/company-skills-routes.test.ts
server/src/__tests__/heartbeat-runtime-skills.test.ts`
- `pnpm exec vitest run
server/src/__tests__/company-skills-service.test.ts`
- `pnpm exec vitest run ui/src/components/IssueProperties.test.tsx -t
"edits existing custom assignee model options from the properties pane"`
- `pnpm --filter @paperclipai/server typecheck`
- GitHub checks are green on `0823957a2`: Build, Canary Dry Run, General
tests, Typecheck + Release Registry, serialized server suites, e2e,
policy/review, Socket, Snyk, and aggregate `verify`.
- Greptile Review succeeded on `0823957a2` with `40 files reviewed, 0
comments added`; GitHub unresolved review threads: 0.
Not run in this heartbeat:
- Browser screenshot capture for the UI changes. This PR intentionally
omits screenshots per the Paperclip task direction not to add design
screenshots/images.
## Risks
- Broad feature branch touching DB, shared contracts, server, and UI;
reviewers should still scan merge conflicts carefully if `master` moves
again before landing.
- Skill version/runtime behavior is sensitive: pinned skill versions
must stay pinned while default selections should continue following the
current version.
- UI polish should get normal reviewer/browser attention before merge
because this PR includes a large Skills Store surface and screenshots
were intentionally omitted.
> 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, GPT-5-based coding agent with tool use and local command
execution.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots (intentionally omitted per PAP-10921 direction)
- [ ] 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>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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