## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - Heartbeat runs are the control-plane record of each agent execution
window.
> - Long-running local agents can exhaust context or stop while still
holding useful next-step state.
> - Operators need that stop reason, next action, and continuation path
to be durable and visible.
> - This pull request adds run liveness metadata, continuation
summaries, and UI surfaces for issue run ledgers.
> - The benefit is that interrupted or long-running work can resume with
clearer context instead of losing the agent's last useful handoff.
## What Changed
- Added heartbeat-run liveness fields, continuation attempt tracking,
and an idempotent `0058` migration.
- Added server services and tests for run liveness, continuation
summaries, stop metadata, and activity backfill.
- Wired local and HTTP adapters to surface continuation/liveness context
through shared adapter utilities.
- Added shared constants, validators, and heartbeat types for liveness
continuation state.
- Added issue-detail UI surfaces for continuation handoffs and the run
ledger, with component tests.
- Updated agent runtime docs, heartbeat protocol docs, prompt guidance,
onboarding assets, and skills instructions to explain continuation
behavior.
- Addressed Greptile feedback by scoping document evidence by run,
excluding system continuation-summary documents from liveness evidence,
importing shared liveness types, surfacing hidden ledger run counts,
documenting bounded retry behavior, and moving run-ledger liveness
backfill off the request path.
## Verification
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
server/src/__tests__/run-continuations.test.ts
server/src/__tests__/run-liveness.test.ts
server/src/__tests__/activity-service.test.ts
server/src/__tests__/documents-service.test.ts
server/src/__tests__/issue-continuation-summary.test.ts
server/src/services/heartbeat-stop-metadata.test.ts
ui/src/components/IssueRunLedger.test.tsx
ui/src/components/IssueContinuationHandoff.test.tsx
ui/src/components/IssueDocumentsSection.test.tsx`
- `pnpm --filter @paperclipai/db build`
- `pnpm exec vitest run server/src/__tests__/activity-service.test.ts
ui/src/components/IssueRunLedger.test.tsx`
- `pnpm --filter @paperclipai/ui typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run server/src/__tests__/activity-service.test.ts
server/src/__tests__/run-continuations.test.ts
ui/src/components/IssueRunLedger.test.tsx`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "treats a
plan document update"`
- `pnpm exec vitest run server/src/__tests__/activity-service.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts -t "activity
service|treats a plan document update"`
- Remote PR checks on head `e53b1a1d`: `verify`, `e2e`, `policy`, and
Snyk all passed.
- Confirmed `public-gh/master` is an ancestor of this branch after
fetching `public-gh master`.
- Confirmed `pnpm-lock.yaml` is not included in the branch diff.
- Confirmed migration `0058_wealthy_starbolt.sql` is ordered after
`0057` and uses `IF NOT EXISTS` guards for repeat application.
- Greptile inline review threads are resolved.
## Risks
- Medium risk: this touches heartbeat execution, liveness recovery,
activity rendering, issue routes, shared contracts, docs, and UI.
- Migration risk is mitigated by additive columns/indexes and idempotent
guards.
- Run-ledger liveness backfill is now asynchronous, so the first ledger
response can briefly show historical missing liveness until the
background backfill completes.
- UI screenshot coverage is not included in this packaging pass;
validation is currently through focused component tests.
> 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-5.4, local tool-use coding agent with terminal, git,
GitHub connector, GitHub CLI, and Paperclip API access.
## 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
- [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
Screenshot note: no before/after screenshots were captured in this PR
packaging pass; the UI changes are covered by focused component tests
listed above.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Loading an instructions file is normal, expected behavior — not worth
logging to stdout/stderr on every run. Warning logs for failed reads
are preserved.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
Persist child-process metadata for local adapter runs, keep detached runs alive when their pid still exists, queue a single automatic retry when the pid is confirmed dead, and clear detached warnings when the original run reports activity again.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
The $AGENT_HOME environment variable was referenced by skills (e.g.
para-memory-files) but never actually set, causing runtime errors like
"/HEARTBEAT.md: No such file or directory" when agents tried to resolve
paths relative to their home directory.
Add agentHome to the paperclipWorkspace context in the heartbeat service
and propagate it as the AGENT_HOME env var in all local adapters.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
Gemini CLI only registers run_shell_command in --approval-mode yolo.
Non-yolo modes don't expose it at all, making Paperclip API calls
impossible. Always pass --approval-mode yolo and remove the now-unused
policy engine code, approval mode config, and UI toggles.
Add a "Paperclip API access note" to the prompt with curl examples
via run_shell_command, since the universal SKILL.md is tool-agnostic.
Also extract structured question events from Gemini assistant messages
to support interactive approval flows.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Update stale doc comment in index.ts to reflect direct ~/.gemini/skills/
injection instead of tmpdir approach
- Remove bare GEMINI_API_KEY/GOOGLE_API_KEY from auth regex to prevent
false positives when those strings appear in assistant output
- Align hello probe sandbox/approvalMode flags with execute.ts
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
GEMINI_CLI_HOME pointed to a tmpdir which broke OAuth auth since the CLI
couldn't find credentials in the real home directory.
Instead, inject Paperclip skills directly into ~/.gemini/skills/ (matching
the pattern used by cursor, codex, pi, and opencode adapters). This lets
the Gemini CLI find both auth credentials and skills in their natural
location without any GEMINI_CLI_HOME override.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Incorporate improvements from PR #13 and #105 into the gemini-local adapter:
- Add detectGeminiAuthRequired() for runtime auth failure detection with
errorCode: "gemini_auth_required" on execution results
- Add isGeminiTurnLimitResult() to detect exit code 53 / turn_limit status
and clear session to prevent stuck sessions on next heartbeat
- Add describeGeminiFailure() for structured error messages from parsed
result events including errors array extraction
- Return parsed resultEvent in resultJson instead of raw stdout/stderr
- Add isRetry guard to prevent stale session ID fallback after retry
- Replace boolean yolo with approvalMode string (default/auto_edit/yolo)
with backwards-compatible config.yolo fallback
- Add sandbox config option (--sandbox / --sandbox=none)
- Add GOOGLE_GENAI_USE_GCA auth detection in environment test
- Consolidate auth detection regex into shared detectGeminiAuthRequired()
- Add gemini-2.0-flash and gemini-2.0-flash-lite model IDs
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Isolate skills injection using a temporary directory mapped via
GEMINI_CLI_HOME, mirroring the claude-local sandbox approach
instead of polluting the global ~/.gemini/skills directory.
- Update the environment probe to use `--output-format stream-json`
so the payload matches the downstream parseGeminiJsonl parser.
- Deduplicate `firstNonEmptyLine` helper by extracting it to a
shared `utils.ts` module.
- Clean up orphaned internal exports and update adapter documentation.
