## 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 runs local adapter processes for agents and streams their
output into heartbeat runs
> - Some adapters can emit a terminal result before all descendant
processes have exited
> - If those descendants keep running, a heartbeat can appear complete
while the process group remains alive
> - Claude local runs need a bounded cleanup path after terminal JSON
output is observed and the child exits
> - This pull request adds terminal-result cleanup support to adapter
process utilities and wires it into the Claude local adapter
> - The benefit is fewer stranded adapter process groups after
successful terminal results
## What Changed
- Added terminal-result cleanup options to `runChildProcess`.
- Tracked child exit plus terminal output before signaling lingering
process groups.
- Added Claude local adapter configuration for terminal result cleanup
grace time.
- Added process cleanup tests covering terminal-output cleanup and noisy
non-terminal runs.
## Verification
- `pnpm install --frozen-lockfile --ignore-scripts`
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts`
- Result: 9 tests passed.
## Risks
- Medium risk: this changes adapter child-process cleanup behavior.
- The cleanup only arms after terminal result detection and child exit,
and it is covered by process-group 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 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 it is not applicable
- [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>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The heartbeat runtime, agent import path, and agent configuration
defaults determine whether work is dispatched safely and predictably.
> - Several accumulated fixes all touched agent execution recovery, wake
routing, import behavior, and runtime concurrency defaults.
> - Those changes need to land together so the heartbeat service and
agent creation defaults stay internally consistent.
> - This pull request groups the runtime/governance changes from the
split branch into one standalone branch.
> - The benefit is safer recovery for stranded runs, bounded high-volume
reads, imported-agent approval correctness, skill-template support, and
a clearer default concurrency policy.
## What Changed
- Fixed stranded continuation recovery so successful automatic retries
are requeued instead of incorrectly blocking the issue.
- Bounded high-volume issue/log reads across issue, heartbeat, agent,
project, and workspace paths.
- Fixed imported-agent approval and instruction-path permission
handling.
- Quarantined seeded worktree execution state during worktree
provisioning.
- Queued approval follow-up wakes and hardened SQL_ASCII heartbeat
output handling.
- Added reusable agent instruction templates for hiring flows.
- Set the default max concurrent agent runs to five and updated related
UI/tests/docs.
## Verification
- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run server/src/__tests__/company-portability.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/heartbeat-comment-wake-batching.test.ts
server/src/__tests__/heartbeat-list.test.ts
server/src/__tests__/issues-service.test.ts
server/src/__tests__/agent-permissions-routes.test.ts
packages/adapter-utils/src/server-utils.test.ts
ui/src/lib/new-agent-runtime-config.test.ts`
- Split integration check: merged this branch first, followed by the
other [PAP-1614](/PAP/issues/PAP-1614) branches, with no merge
conflicts.
- Confirmed this branch does not include `pnpm-lock.yaml`.
## Risks
- Medium risk: touches heartbeat recovery, queueing, and issue list
bounds in central runtime paths.
- Imported-agent and concurrency default behavior changes may affect
existing automation that assumes one-at-a-time default runs.
- No database migrations are included.
> 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 tool-enabled coding model, agentic
code-editing/runtime with local shell and GitHub CLI access; exact
context window and reasoning mode are not exposed by the Paperclip
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 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
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## 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>
## Thinking Path
> - Paperclip orchestrates AI agents via adapters (`claude_local`,
`codex_local`, etc.)
> - Each adapter type has different capabilities — instructions bundles,
skill materialization, local JWT — but these were gated by 5 hardcoded
type lists scattered across server routes and UI components
> - External adapter plugins (e.g. a future `opencode_k8s`) cannot add
themselves to those hardcoded lists without patching Paperclip source
> - The existing `supportsLocalAgentJwt` field on `ServerAdapterModule`
proves the right pattern already exists; it just wasn't applied to the
other capability gates
> - This pull request replaces the 4 remaining hardcoded lists with
declarative capability flags on `ServerAdapterModule`, exposed through
the adapter listing API
> - The benefit is that external adapter plugins can now declare their
own capabilities without any changes to Paperclip source code
## What Changed
- **`packages/adapter-utils/src/types.ts`** — added optional capability
fields to `ServerAdapterModule`: `supportsInstructionsBundle`,
`instructionsPathKey`, `requiresMaterializedRuntimeSkills`
- **`server/src/routes/agents.ts`** — replaced
`DEFAULT_MANAGED_INSTRUCTIONS_ADAPTER_TYPES` and
`ADAPTERS_REQUIRING_MATERIALIZED_RUNTIME_SKILLS` hardcoded sets with
capability-aware helper functions that fall back to the legacy sets for
adapters that don't set flags
- **`server/src/routes/adapters.ts`** — `GET /api/adapters` now includes
a `capabilities` object per adapter (all four flags + derived
`supportsSkills`)
- **`server/src/adapters/registry.ts`** — all built-in adapters
(`claude_local`, `codex_local`, `process`, `cursor`) now declare flags
explicitly
- **`ui/src/adapters/use-adapter-capabilities.ts`** — new hook that
fetches adapter capabilities from the API
- **`ui/src/pages/AgentDetail.tsx`** — replaced hardcoded `isLocal`
allowlist with `capabilities.supportsInstructionsBundle` from the API
- **`ui/src/components/AgentConfigForm.tsx`** /
**`OnboardingWizard.tsx`** — replaced `NONLOCAL_TYPES` denylist with
capability-based checks
- **`server/src/__tests__/adapter-registry.test.ts`** /
**`adapter-routes.test.ts`** — tests covering flag exposure,
undefined-when-unset, and per-adapter values
- **`docs/adapters/creating-an-adapter.md`** — new "Capability Flags"
section documenting all flags and an example for external plugin authors
## Verification
- Run `pnpm test --filter=@paperclip/server -- adapter-registry
adapter-routes` — all new tests pass
- Run `pnpm test --filter=@paperclip/adapter-utils` — existing tests
still pass
- Spin up dev server, open an agent with `claude_local` type —
instructions bundle tab still visible
- Create/open an agent with a non-local type — instructions bundle tab
still hidden
- Call `GET /api/adapters` and verify each adapter includes a
`capabilities` object with the correct flags
## Risks
- **Low risk overall** — all new flags are optional with
backwards-compatible fallbacks to the existing hardcoded sets; no
adapter behaviour changes unless a flag is explicitly set
- Adapters that do not declare flags continue to use the legacy lists,
so there is no regression risk for built-in adapters
- The UI capability hook adds one API call to AgentDetail mount; this is
a pre-existing endpoint, so no new latency path is introduced
## Model Used
- Provider: Anthropic
- Model: Claude Sonnet 4.6 (`claude-sonnet-4-6`)
- Context: 200k token context window
- Mode: Agentic tool use (code editing, bash, grep, file reads)
## 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 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
---------
Co-authored-by: Pawla Abdul (Bot) <pawla@groombook.dev>
Co-authored-by: Paperclip <noreply@paperclip.ing>
- Fix external adapters (hermes, droid) not auto-selected when
navigating with ?adapterType= param — was using a stale
module-level Set built before async adapter registration
- Move SchemaConfigFields to render after thinking effort (same
visual area as Claude's chrome toggle) instead of bottom of
config section
- Extract SelectField into its own component to fix React hooks
order violation when schema fields change between renders
- Add onAdapterChange() subscription in registry.ts so
registerUIAdapter() notifies components when dynamic parsers
load, fixing stale parser for old runs
- Add parserTick to both RunTranscriptView and
useLiveRunTranscripts to force recomputation on parser change
- Plugin loader: install/reload/remove/reinstall external adapters
from npm packages or local directories
- Plugin store persisted at ~/.paperclip/adapter-plugins.json
- Self-healing UI parser resolution with version caching
- UI: Adapter Manager page, dynamic loader, display registry
with humanized names for unknown adapter types
- Dev watch: exclude adapter-plugins dir from tsx watcher
to prevent mid-request server restarts during reinstall
- All consumer fallbacks use getAdapterLabel() for consistent display
- AdapterTypeDropdown uses controlled open state for proper close behavior
- Remove hermes-local from built-in UI (externalized to plugin)
- Add docs for external adapters and UI parser contract
Avoid relying on ComSpec for .cmd/.bat invocation in runChildProcess. Some Win11 environments set ComSpec to PowerShell, which breaks cmd-specific flags (/d /s /c) and causes adapter CLI discovery failures (e.g. opencode models).
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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>
When tool_result entries arrive without a matching tool_call, the transcript
was showing generic 'tool' as the name. Now pl-local parses toolName from
tool_execution_end events and passes it through, so the UI can display
the actual tool name (e.g., 'bash', 'Read', 'Ls') instead of 'tool'.
Expose adapter-discovered user-installed skills with provenance metadata, share persistent skill snapshot classification across local adapters, and render unmanaged skills as a read-only section in the agent skills UI.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
- Extract all Anthropic credential/API logic into claude-local/src/server/quota.ts
- Extract all OpenAI/WHAM credential/API logic into codex-local/src/server/quota.ts
- Add optional getQuotaWindows() to ServerAdapterModule in adapter-utils
- Rewrite quota-windows.ts as a 29-line thin aggregator with zero provider knowledge
- Wire getQuotaWindows into adapter registry for claude-local and codex-local
- Add 47 unit tests covering toPercent, secondsToWindowLabel, WHAM normalization,
readClaudeToken, readCodexToken, fetchClaudeQuota, fetchCodexQuota, fetchWithTimeout
- Add 8 unit tests covering parseDateRange validation and byProvider pro-rata math
Adding a third provider now requires only touching that provider's adapter.
* public-gh/master:
Default Gemini adapter to yolo mode and add API access prompt note
fix: remove Cmd+1..9 company-switch shortcut
fix(ui): prevent IME composition Enter from moving focus in new issue title
fix(cli): add restart hint after allowed-hostname change
docs: remove obsolete TODO for CONTRIBUTING.md
fix: default dangerouslySkipPermissions to true for unattended agents
fix: route heartbeat cost recording through costService
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