## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Agents run in heartbeat runs orchestrated by the server; run
lifecycle, retry scheduling, and the dashboard's run-activity metrics
are the subsystems involved
> - A spike in "failed" tasks traced to three causes: server restarts
killing in-flight runs and mislabeling them as failures, deterministic
workspace-validation loops when a worktree's branch diverged, and
provider quota/usage-limit errors being classified as generic transient
failures (putting agents into error state and polluting metrics)
> - Killed-then-recovered runs and quota waits are not product failures,
so both the runtime behavior and the reporting needed to distinguish
them
> - This pull request drains runs gracefully on shutdown with idempotent
restart retries, self-heals workspace branch mismatches, adds a
quota-aware failure class with reset-time retry, separates recovered
restart kills from true failures on the dashboard, and documents restart
hygiene for operators
> - The benefit is fewer spurious failures, automatic recovery instead
of manual repair, and dashboard metrics that reflect real failure rates
## Linked Issues or Issue Description
No public GitHub issue exists; describing the bug inline per the
bug-report template:
**What happened?**
In-flight heartbeat runs are marked `failed` when the server restarts,
even though a retry later succeeds. Worktrees whose checked-out branch
diverges from the issue branch fail workspace validation on every
subsequent run with no recovery path. Provider quota/usage-limit
responses are treated as generic transient upstream errors, putting
agents into an error state and retrying before the quota window resets.
The dashboard counts all of these as true failures, inflating failure
metrics.
**Expected behavior**
Graceful shutdown should interrupt (not fail) running runs and chain
exactly one recovery retry. Workspace validation should repair
recoverable branch mismatches automatically. Quota errors should get
their own error class with the retry scheduled at the provider reset
time and the agent left idle. The dashboard should report recovered
restart kills separately from true failures.
**Steps to reproduce**
1. Start a heartbeat run, then restart the server (SIGTERM) while it is
in flight — the run lands as `failed` with a process-loss error code
even when its retry succeeds
2. Check out an issue whose worktree branch has diverged (e.g. after a
force-moved branch) — every subsequent run fails
`workspace_validation_failed` deterministically
3. Drive an agent into a provider usage-limit window — the run fails as
a generic transient upstream error and the agent enters an error state
instead of idling until the reset time
**Paperclip version or commit**
master (base c07e650cd)
**Deployment mode**
Self-hosted dev plane (Linux, node server + embedded Postgres)
## What Changed
- Graceful shutdown (SIGTERM hook) now marks in-flight runs
`interrupted` instead of `failed` and enqueues an idempotent
process-loss retry (pre-insert existence check on `retryOfRunId`
prevents duplicates; bursts chain exactly one retry per interrupted run)
- Run-liveness classification routes `interrupted` to `needs_followup`
rather than `failed`
- Workspace validation self-heals branch mismatch / missing-branch
states instead of failing deterministically on every run
- New `provider_quota` error class: session/usage-limit responses
schedule the retry at the provider reset time and leave the agent idle
(not errored); fixes a case where a quota-terminated run with subtype
`success` was misclassified as failed; HTTP 529 remains transient
- Dashboard run-activity query separates recovered restart kills from
true failures via a recursive CTE over `retry_of_run_id` (ancestors of a
succeeded retry count as recovered), adds a per-day failed-by-error-code
breakdown, and binds the window start as a timestamptz string
- Activity charts UI: amber "Recovered" segment with legend and per-day
error-code tooltip; success-rate chart counts recovered runs as
successes
- New ops runbook: `docs/deploy/dev-plane-restart-hygiene.md`
## Verification
- Greptile follow-up fixes on `992705edd`: `pnpm exec vitest run
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/heartbeat-workspace-branch-containment.test.ts
server/src/__tests__/heartbeat-workspace-session.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/heartbeat-workspace-finalize-branch.test.ts` (209
tests); `pnpm --filter @paperclipai/server typecheck`; `git diff
--check`
- Post-rebase CI fixes: `pnpm exec vitest run
server/src/__tests__/heartbeat-retry-scheduling.test.ts`; `pnpm exec
vitest run server/src/__tests__/heartbeat-retry-scheduling.test.ts
server/src/__tests__/workspace-runtime.test.ts
server/src/__tests__/heartbeat-workspace-branch-containment.test.ts
server/src/__tests__/heartbeat-workspace-finalize-branch.test.ts
server/src/__tests__/heartbeat-workspace-session.test.ts` (227 tests);
`pnpm --filter @paperclipai/server typecheck`
- `npm test` server suites covering the changes:
`heartbeat-process-recovery`, `heartbeat-stop-metadata`,
`heartbeat-retry-scheduling` (95 tests), quota parse +
execute/retry-scheduling suites (100 tests), workspace self-heal suites
(200 tests), dashboard run-activity tests (3 tests) — all green,
typecheck exit 0
- Dashboard CTE cross-checked against a real development database: two
restart-burst days moved from 17 to 8 and 19 to 6 true failures once
recovered kills were separated, matching manual retry-chain inspection
- Screenshot verification of the real ActivityCharts component
(recovered segment + tooltip) during QA
## Risks
- Behavioral shift: runs killed by a restart no longer surface as
`failed`; anyone consuming raw run statuses will see `interrupted` (new
status value) — dashboards/queries in this repo were updated accordingly
- Retry chaining on repeated restarts is bounded (one chained retry per
interruption) but a pathological restart loop still delays work rather
than failing it; the runbook covers operator hygiene for that case
- Dashboard query adds a recursive CTE; cost is bounded by the
day-window row count and was verified against production-sized data
- No schema migrations; low migration risk
## Model Used
- Claude (Anthropic) — claude-fable-5 via Claude Code / Paperclip agent
harness, extended thinking with tool use; implementation commits also
produced with Codex CLI (GPT-5 class) agents under the same harness
## 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>
## 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 orchestrates AI agents through issue checkout, heartbeat
runs, routines, and auditable control-plane state
> - The runtime path has to recover from lost local processes, transient
adapter failures, blocked dependencies, and routine coalescing without
stranding work
> - The existing branch carried several reliability fixes across
heartbeat scheduling, issue runtime controls, routine dispatch, and
operator-facing run state
> - These changes belong together because they share backend contracts,
migrations, and runtime status semantics
> - This pull request groups the control-plane/runtime slice so it can
merge independently from board UI polish and adapter sandbox work
> - The benefit is safer heartbeat recovery, clearer runtime controls,
and more predictable recurring execution behavior
## What Changed
- Adds bounded heartbeat retry scheduling, scheduled retry state, and
Codex transient failure recovery handling.
- Tightens heartbeat process recovery, blocker wake behavior, issue
comment wake handling, routine dispatch coalescing, and
activity/dashboard bounds.
- Adds runtime-control MCP tools and Paperclip skill docs for issue
workspace runtime management.
- Adds migrations `0061_lively_thor_girl.sql` and
`0062_routine_run_dispatch_fingerprint.sql`.
- Surfaces retry state in run ledger/agent UI and keeps related shared
types synchronized.
## Verification
- `pnpm exec vitest run
server/src/__tests__/heartbeat-retry-scheduling.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/routines-service.test.ts`
- `pnpm exec vitest run src/tools.test.ts` from `packages/mcp-server`
## Risks
- Medium risk: this touches heartbeat recovery and routine dispatch,
which are central execution paths.
- Migration order matters if split branches land out of order: merge
this PR before branches that assume the new runtime/routine fields.
- Runtime retry behavior should be watched in CI and in local operator
smoke tests because it changes how transient failures are resumed.
> 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 runtime, shell/git tool use
enabled. Exact hosted model build and context window are not exposed in
this Paperclip heartbeat environment.
## 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 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
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Thinking Path
> - Paperclip gives operators a live view of agent work across
dashboards, transcripts, and run activity charts
> - Those views consume live run updates and aggregate run activity from
backend dashboard data
> - Missing or partial run data could make charts brittle, and live
transcript updates were heavier than needed
> - Operators need dashboard data to stay stable even when recent run
payloads are incomplete
> - This pull request hardens dashboard run aggregation, guards chart
rendering, and lightens live run update handling
> - The benefit is a more reliable dashboard during active agent
execution
## What Changed
- Added dashboard run activity types and backend aggregation coverage.
- Guarded activity chart rendering when run data is missing or partial.
- Reduced live transcript update churn in active agent and run chat
surfaces.
- Fixed issue chat avatar alignment in the thread renderer.
- Added focused dashboard, activity chart, and live transcript tests.
## Verification
- `pnpm install --frozen-lockfile --ignore-scripts`
- `pnpm exec vitest run server/src/__tests__/dashboard-service.test.ts
ui/src/components/ActivityCharts.test.tsx
ui/src/components/transcript/useLiveRunTranscripts.test.tsx`
- Result: 8 tests passed, 1 skipped. The embedded Postgres dashboard
service test skipped on this host with the existing PGlite/Postgres init
warning; UI chart and transcript tests passed.
## Risks
- Medium-low risk: aggregation semantics changed, but the UI remains
guarded around incomplete data.
- The dashboard service test is host-skipped here, so CI should confirm
the embedded database path.
> 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, tool-enabled local shell and
GitHub workflow, exact runtime context window 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots, or documented why targeted component tests are sufficient
here
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Dotta