## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The experimental Paperclip Runner can execute a guarded Codex run
and persist provider-neutral events.
> - The task page still reads direct-adapter transcripts and cannot
present those native events.
> - Structured runner questions must also use the existing task
interaction experience.
> - Runtime selection must use the persisted run mode, not an adapter
name or a current feature flag.
> - This pull request projects native events and questions into the
existing task thread.
> - Direct adapters keep their existing transcript, composer,
interaction, and finalization paths.
> - The benefit is a complete native Codex task thread without a
behavior change for existing adapters.
## Linked Issues or Issue Description
Refs #12202. This pull request replaces that stale implementation on
current `master`.
**What happened?**
The server persists native runner events and structured input requests.
The task page only consumes direct-adapter transcripts. A native run
therefore cannot present a complete transcript, usage, or question flow
through the normal task experience.
**Expected behavior**
Native runs project persisted provider-neutral events into the existing
task thread. Native structured questions use the existing interaction
card. Direct adapters retain their current behavior.
**Steps to reproduce**
1. Enable the experimental runner.
2. Start a native Codex run that emits progress, usage, a structured
question, and a final reply.
3. Open the task page.
4. Observe that the direct-adapter transcript path cannot project the
native event records.
**Paperclip version or commit**
`master` at `67f9867bc`.
## What Changed
- Add the canonical structured-question validator and shared contract
exports.
- Materialize native input requests as existing task interactions.
- Validate native answers and deliver them through the durable
question-response receipt.
- Resume the original PRP request with an idempotent `request.resolve`
command.
- Project native messages, tool activity, cumulative usage, and final
replies into the existing transcript model.
- Propagate persisted `runtimeMode` to the task page and select native
handling only for `runtimeMode: "native"`.
- Expire pending interactions through the shared issue service on every
terminal transition, including decisions, stalled reviews, tree control,
and pipeline retry cleanup.
- Queue native run cancellation while a transaction is open and execute
it only after the owning transaction commits.
- Keep nonterminal and non-runner issue paths on their existing service
call shapes and behavior.
## Verification
- `pnpm --filter @paperclipai/server typecheck` — passed, including the
Rust runner release build and protocol/catalog drift gates.
- Focused native-thread and lifecycle suites — 18 files and 481 tests
passed during review.
- `issue-execution-policy-routes.test.ts` — 19/19 passed after the final
transactional-queue expectation update.
- `issue-agent-mutation-ownership-routes.test.ts` — 87/87 passed in the
final isolated compatibility rerun.
- GitHub Actions — policy, build, canary, typecheck/release registry, 5
serialized server shards, 8 general-test shards, 3 browser shards, and
both aggregate gates passed on `7793f3193`.
- Security — Snyk, Socket Project Report, Socket PR Alerts, and
Superagent passed.
- Greptile — 5/5 on `7793f3193`; all actionable review threads resolved.
- `git diff --check` — passed.
- Diff against `master`: 44 files.
## Compatibility Boundary
- Native transcript polling only runs when the persisted run reports
`runtimeMode: "native"`.
- Missing or legacy runtime modes continue through
`useLiveRunTranscripts`.
- Legacy questions keep the existing optional free-text choice.
- Native closed select sets can suppress that legacy fallback.
- Terminal cleanup uses the same issue service for native and legacy
interactions; only a bound native question schedules a native run
cancellation.
- Native cancellation happens after transaction commit, so failed or
rolled-back writes do not cancel a still-valid run.
- The durable delivery service checks the original native request before
it considers a continuation run.
- This pull request adds no migration, dependency, workflow, manifest,
or lockfile change.
## Risks
The main risk is routing a direct-adapter task through native handling
or changing terminal issue behavior. The implementation selects the
native path only from persisted runtime facts, retains the existing
nonterminal call shape, and schedules native cancellation only for a
validated bound native question after commit. Focused and
repository-wide tests cover both paths. Native requests remain bound to
the company, issue, run, and agent; answers are validated, durable, and
idempotent across reconnects.
## Model Used
OpenAI Codex, GPT-5 family. The client does not expose the exact
deployment ID or context window. Agentic reasoning, tool use, and code
execution were 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] 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 and contains no internal
Paperclip ticket id or instance-derived details
- [x] I have run the affected local tests and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated the compatibility notes for this change
- [x] I have considered and documented risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I addressed all Greptile and reviewer comments before requesting
merge
## 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.
> - Pipeline automations let operators standardize repeated issue and
workflow actions.
> - Pipeline-created issues currently need a way to derive useful titles
from routine variables.
> - Without a configurable title template, automated pipeline output is
harder to scan and distinguish.
> - This pull request adds a title-template field through shared
contracts, server persistence, API routes, and the pipeline settings UI.
> - The benefit is clearer issue titles for pipeline-created work while
preserving the existing pipeline behavior when no template is
configured.
## Linked Issues or Issue Description
Refs #8790
This PR adds configurable generated-issue title templates for pipeline
automations.
## What Changed
- Added `issueTitleTemplate` to the shared pipeline automation contract
and field constants.
- Persisted and returned the title template through pipeline service and
route code.
- Applied title-template rendering when pipeline automations create
issue work.
- Added pipeline settings UI controls for editing the title template and
reusing routine variables.
- Moved title-token cursor restoration out of the React state updater
and into a layout effect.
- Added server and UI coverage for storing, returning, and rendering
pipeline title templates.
## Verification
- `NODE_ENV=test pnpm run preflight:workspace-links && NODE_ENV=test
pnpm exec vitest run server/src/__tests__/pipelines-service.test.ts
server/src/__tests__/pipelines-routes.test.ts
ui/src/pages/PipelineSettings.test.ts`
- Result before review follow-up: 3 files passed, 58 tests passed.
- `pnpm --filter @paperclipai/ui exec vitest run
src/pages/PipelineSettings.test.ts`
- Result after review follow-up: 1 file passed, 7 tests passed.
- Branch was merged with current `paperclipai:master` at `f019f54bb3`
before opening this PR.
- Searched existing PRs for the same head branch and for pipeline
title-template duplicates; no matching existing PR was found.
- Note: GitHub could not open a PR directly from `cryppadotta/paperclip`
because that repository is not a fork of `paperclipai/paperclip`. The
same updated branch SHA was pushed to `paperclipai/paperclip` so this PR
can compare normally against `master`.
## Risks
Low to moderate risk. The change touches pipeline automation persistence
and generated issue creation, so regressions would most likely appear as
missing or incorrectly rendered generated issue titles. Existing
behavior should remain unchanged when `issueTitleTemplate` is unset.
## Model Used
OpenAI Codex, GPT-5-based coding agent, tool-enabled execution in a
Paperclip heartbeat, with repository inspection, Git, GitHub CLI, and
local test 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 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
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The pipeline subsystem models repeatable work as items moving
through stages, with agent automation, review gates, blockers, drift
notices, and linked work.
> - Operators need this to be usable as one coherent workflow surface,
not just as backend primitives or disconnected route experiments.
> - The branch now carries the pipeline data model, service/routes,
CLI/tutorial path, aggregation feeds, operator UI, stage automation
controls, liveness/retry handling, and follow-up polish that make the
primitive reviewable end to end.
> - This pull request is the single review target for that pipeline
workflow primitive stack.
> - The benefit is that reviewers can evaluate the full operator
experience and server contract together against `master`.
## Linked Issues or Issue Description
No public GitHub issue exists for this work. The underlying feature
request is described inline.
### Problem or motivation
Paperclip needs a first-class way to model multi-stage agent/company
workflows where upstream items can spawn downstream work, request
review, carry fields across pipelines, surface drift, retry automation,
and show operators where work is blocked or active. Without a unified
pipeline primitive, these workflows spread across ad hoc issues,
routines, and comments, making the state hard to inspect or operate.
### Proposed solution
Add the pipeline workflow primitive stack: database schema and
migrations, shared validators/types, server services and REST routes,
aggregation and liveness helpers, CLI/tutorial smoke support, and the
React operator UI for pipeline lists, boards, item detail,
review/learnings views, settings, stage automation, secrets, carry-over
fields, and retry/recovery flows.
### Alternatives considered
- Keep workflows as loosely linked issues and routines: rejected because
operators need a single board/detail/settings surface for repeated
workflow patterns.
- Ship backend primitives first and defer UI: rejected for this branch
because the operator experience is the main way to validate the
primitive.
- Add a narrower one-off content workflow: rejected because the same
primitives are useful across future company processes.
## What Changed
- Added and evolved pipeline schema, migrations, shared contracts,
server services, REST routes, route tests, and CLI/tutorial smoke
support.
- Added pipeline aggregation, health/liveness, drift acknowledgment,
blocker/carry-over, automation retry, stage automation environment, and
permission recovery behavior.
- Added the operator UI for pipeline index/board/item
detail/settings/review/learnings flows, including stage secrets,
automation controls, markdown/item descriptions, linked issue assets,
liveness banners, and source automation metadata.
- Refactored issue document frame rendering through the shared
`DocumentFrameHeader` component to keep document controls consistent
with the pipeline document surfaces.
- Kept this PR as the single base-branch review target for the current
pipeline branch.
## Verification
Current branch refresh:
- `pnpm vitest run server/src/__tests__/pipelines-service.test.ts` — 31
passed
- `pnpm vitest run server/src/__tests__/pipelines-routes.test.ts` — 19
passed
- `pnpm --filter ./server typecheck` — passed
- `pnpm --filter ./ui typecheck` — passed
- Verified Pipelines remains gated by `enablePipelines === true`:
sidebar item is hidden unless the flag is enabled, direct pipeline
routes redirect to `/dashboard` when disabled, and the Experimental
settings UI still has no Pipelines toggle.
- GitHub status checks on `df071c710646de625131064c3fb6588b5e97964a` —
all complete with no failing conclusions, including Actions, Socket,
Superagent/Security, and Greptile Review
- Greptile summary on `df071c710646de625131064c3fb6588b5e97964a` —
Confidence Score 5/5
- GitHub review-thread sweep — 0 unresolved Greptile threads
Previously recorded during branch development:
- Server pipeline service/route and aggregation tests
- Shared validator tests
- UI pipeline page/settings/item-detail/learnings/liveness tests
- Pipeline tutorial smoke path
## Risks
- High review surface: this is a large feature branch spanning database,
shared contracts, server behavior, CLI/docs, and UI.
- Migration ordering and schema compatibility need reviewer attention
because this branch has been kept current across multiple `master`
syncs.
- GitHub still reports merge state `BLOCKED` because the PR is awaiting
normal human review/branch-protection completion; all current status
checks are green.
- Branch-name checklist exception: this PR uses the pre-existing
requested branch name, which predates the current public-branch naming
rule. The PR title/body avoid internal issue references.
> 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 coding agent based on GPT-5, with repository tool use,
shell execution, git/GitHub CLI operations, and local verification
commands. Earlier commits in this branch were assisted by Paperclip
agents and other AI coding agents as recorded in commit authorship.
## 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)
- [ ] 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>
Dotta