## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - Agents run inside environments (local, SSH, E2B sandbox)
> - Operators need to configure and manage these environments
> - But environment settings were buried inside the general company
settings page, making them hard to find
> - Additionally, when testing an agent from the configuration form, the
test always ran locally regardless of which environment was selected
> - This PR moves environments into a dedicated top-level company
settings section and wires the "Test Environment" button to run inside
the selected environment
> - The benefit is operators can find and manage environments more
easily, and the test button now validates the actual environment the
agent will use
## What Changed
- Added a dedicated `CompanyEnvironments` settings page with its own
route and sidebar entry
- Updated `CompanySettingsSidebar` and `CompanySettingsNav` to include
the new environments section
- Modified the agent test route (`POST /agents/:id/test`) to accept an
optional `environmentId` parameter
- Updated all adapter `test.ts` handlers to resolve and use the
specified execution target environment
- Added `resolveTestExecutionTarget` to `execution-target.ts` for remote
environment test resolution with cwd fallback
- Moved the "Test Environment" button and its feedback display into the
`NewAgent` page footer for better UX flow
## Verification
- `pnpm test` — all existing and new tests pass
- `pnpm typecheck` — clean
- Manual: navigate to Company Settings, confirm "Environments" appears
as a top-level section
- Manual: configure an agent with a non-local environment, click "Test
Environment", confirm the test runs inside that environment
## Risks
- Low risk. UI-only routing change for the settings page. The
test-in-environment change adds an optional parameter with a local
fallback, so existing behavior is preserved when no environment is
specified.
## Model Used
Codex GPT 5.4 high via Paperclip.
## 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
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The local adapter layer is responsible for turning Paperclip runtime
context into the environment seen by the child agent process.
> - The CEO onboarding bundle tells the agent where to read and write
its persistent memory and fact files.
> - That bundle was using `./memory/...` and `./life/...`, which only
works when the process cwd happens to equal the agent home directory.
> - At the same time, six local adapters each duplicated the same
workspace-env propagation logic, including `AGENT_HOME`, which makes
this contract easy to drift.
> - This pull request fixes the CEO instructions to use
`$AGENT_HOME/...` and centralizes workspace-env propagation in one
shared helper with shared tests.
> - The benefit is a real bug fix for agent memory paths plus a single
tested contract that makes future built-in adapter work less likely to
forget `AGENT_HOME`.
## What Changed
- Updated `server/src/onboarding-assets/ceo/HEARTBEAT.md` to use
`$AGENT_HOME/memory/...` and `$AGENT_HOME/life/...` instead of
cwd-relative `./memory/...` and `./life/...`.
- Added `applyPaperclipWorkspaceEnv(...)` in
`packages/adapter-utils/src/server-utils.ts` to centralize
`PAPERCLIP_WORKSPACE_*` and `AGENT_HOME` propagation.
- Added shared helper coverage in
`packages/adapter-utils/src/server-utils.test.ts` for both populated and
skip-empty cases.
- Switched the built-in local adapters (`claude_local`, `codex_local`,
`cursor_local`, `gemini_local`, `opencode_local`, `pi_local`) over to
the shared helper instead of inline env assignment blocks.
## Verification
- `pnpm install`
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
packages/adapters/claude-local/src/server/execute.remote.test.ts
packages/adapters/codex-local/src/server/execute.remote.test.ts
packages/adapters/cursor-local/src/server/execute.remote.test.ts
packages/adapters/gemini-local/src/server/execute.remote.test.ts
packages/adapters/opencode-local/src/server/execute.remote.test.ts
packages/adapters/pi-local/src/server/execute.remote.test.ts`
- Result: 7 test files passed, 31 tests passed, 0 failures.
## Risks
- Low risk.
- The only behavioral surface is the shared env propagation refactor
across six adapters; if the helper diverged from prior semantics, an
adapter could miss a workspace env var.
- The shared helper test plus the affected adapter execute tests reduce
that risk, and the helper preserves the prior "set only non-empty
strings" behavior.
## Model Used
- OpenAI Codex via Paperclip `codex_local` agent runtime; tool-assisted
coding workflow with shell execution, file patching, git operations, and
API interaction. The exact backend model identifier and context window
are not surfaced by this local 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 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
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - Agents working on the Paperclip codebase itself need guidance on dev
workflows: server lifecycle, worktrees, builds, database ops,
diagnostics
> - There was no bundled skill covering these workflows — agents had to
figure it out from scratch each time
> - Additionally, not every skill should be force-installed on every
agent — a dev-focused skill should be opt-in
> - This PR adds a `paperclip-dev` skill with `required: false`
frontmatter so it ships with Paperclip but isn't auto-installed
> - The skill's PR section references canonical files
(`.github/PULL_REQUEST_TEMPLATE.md`, `CONTRIBUTING.md`) instead of
duplicating their content, with gated instructions that force agents to
read those files before creating any PR
> - The benefit is that developers (human or agent) can opt in to
structured dev guidance without polluting the default agent skill set or
creating drift between duplicated docs
## What Changed
- Added `skills/paperclip-dev/SKILL.md` covering server management,
worktree lifecycle, builds, database ops, diagnostics, agent operations,
and common mistakes
- The Pull Requests section uses gated, reference-based instructions —
agents MUST read `.github/PULL_REQUEST_TEMPLATE.md` and
`CONTRIBUTING.md` before running `gh pr create`, with a brief checklist
of required section names (no content duplication)
- Updated `packages/adapter-utils/src/server-utils.ts` to respect
`required: false` frontmatter — optional skills are bundled but not
auto-installed on agents
- Added test in `server/src/__tests__/paperclip-skill-utils.test.ts`
verifying that optional skills are excluded from the default install set
## Verification
```bash
# Run tests
pnpm test
# Manual verification: create a fresh worktree without seeding
npx paperclipai worktree:make test-optional-skill --no-seed
cd ~/paperclip-test-optional-skill
eval "$(npx paperclipai worktree env)"
npx paperclipai run
# Verify paperclip-dev appears in company skill library but is NOT auto-assigned
# Call listPaperclipSkillEntries() — paperclip-dev should show required: false
# Call resolvePaperclipDesiredSkillNames() — paperclip-dev should NOT be in the default set
# Cleanup
npx paperclipai worktree:cleanup test-optional-skill
```
## Risks
- Low risk. The `required` field defaults to `true` when absent, so all
existing skills behave identically. Only the new `paperclip-dev` skill
sets `required: false`.
## Model Used
Claude Opus 4.6 (`claude-opus-4-6`) via Claude Code, with tool use and
extended context.
## 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: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The environment/runtime layer decides where agent work executes and
how the control plane reaches those runtimes.
> - Today Paperclip can run locally and over SSH, but sandboxed
execution needs a first-class environment model instead of one-off
adapter behavior.
> - We also want sandbox providers to be pluggable so the core does not
hardcode every provider implementation.
> - This branch adds the Sandbox environment path, the provider
contract, and a deterministic fake provider plugin.
> - That required synchronized changes across shared contracts, plugin
SDK surfaces, server runtime orchestration, and the UI
environment/workspace flows.
> - The result is that sandbox execution becomes a core control-plane
capability while keeping provider implementations extensible and
testable.
## What Changed
- Added sandbox runtime support to the environment execution path,
including runtime URL discovery, sandbox execution targeting,
orchestration, and heartbeat integration.
- Added plugin-provider support for sandbox environments so providers
can be supplied via plugins instead of hardcoded server logic.
- Added the fake sandbox provider plugin with deterministic behavior
suitable for local and automated testing.
- Updated shared types, validators, plugin protocol definitions, and SDK
helpers to carry sandbox provider and workspace-runtime contracts across
package boundaries.
- Updated server routes and services so companies can create sandbox
environments, select them for work, and execute work through the sandbox
runtime path.
- Updated the UI environment and workspace surfaces to expose sandbox
environment configuration and selection.
- Added test coverage for sandbox runtime behavior, provider seams,
environment route guards, orchestration, and the fake provider plugin.
## Verification
- Ran locally before the final fixture-only scrub:
- `pnpm -r typecheck`
- `pnpm test:run`
- `pnpm build`
- Ran locally after the final scrub amend:
- `pnpm vitest run server/src/__tests__/runtime-api.test.ts`
- Reviewer spot checks:
- create a sandbox environment backed by the fake provider plugin
- run work through that environment
- confirm sandbox provider execution does not inherit host secrets
implicitly
## Risks
- This touches shared contracts, plugin SDK plumbing, server runtime
orchestration, and UI environment/workspace flows, so regressions would
likely show up as cross-layer mismatches rather than isolated type
errors.
- Runtime URL discovery and sandbox callback selection are sensitive to
host/bind configuration; if that logic is wrong, sandbox-backed
callbacks may fail even when execution succeeds.
- The fake provider plugin is intentionally deterministic and
test-oriented; future providers may expose capability gaps that this
branch does not yet cover.
## Model Used
- OpenAI Codex coding agent on a GPT-5-class backend in the
Paperclip/Codex harness. Exact backend model ID is not exposed
in-session. Tool-assisted workflow with shell execution, file editing,
git history inspection, 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 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 orchestrates AI agents for zero-human companies
> - Adapter execution and retry classification decide whether agent work
pauses, retries, or recovers automatically
> - Transient provider failures need to be classified precisely so
Paperclip does not convert retryable upstream conditions into false hard
failures
> - At the same time, operators need an up-to-date model list for
Codex-backed agents and prompts should nudge agents toward targeted
verification instead of repo-wide sweeps
> - This pull request tightens transient recovery classification for
Claude and Codex, updates the agent prompt guidance, and adds Codex
model refresh support end-to-end
> - The benefit is better automatic retry behavior plus fresher
operator-facing model configuration
## What Changed
- added Codex usage-limit retry-window parsing and Claude extra-usage
transient classification
- normalized the heartbeat transient-recovery contract across adapter
executions and heartbeat scheduling
- documented that deferred comment wakes only reopen completed issues
for human/comment-reopen interactions, while system follow-ups leave
closed work closed
- updated adapter-utils prompt guidance to prefer targeted verification
- added Codex model refresh support in the server route, registry,
shared types, and agent config form
- added adapter/server tests covering the new parsing, retry scheduling,
and model-refresh behavior
## Verification
- `pnpm exec vitest run --project @paperclipai/adapter-utils
packages/adapter-utils/src/server-utils.test.ts`
- `pnpm exec vitest run --project @paperclipai/adapter-claude-local
packages/adapters/claude-local/src/server/parse.test.ts`
- `pnpm exec vitest run --project @paperclipai/adapter-codex-local
packages/adapters/codex-local/src/server/parse.test.ts`
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/adapter-model-refresh-routes.test.ts
server/src/__tests__/adapter-models.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/heartbeat-retry-scheduling.test.ts`
## Risks
- Moderate behavior risk: retry classification affects whether runs
auto-recover or block, so mistakes here could either suppress needed
retries or over-retry real failures
- Low workflow risk: deferred comment wake reopening is intentionally
scoped to human/comment-reopen interactions so system follow-ups do not
revive completed issues unexpectedly
> 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 code execution
in the Codex CLI 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
- [ ] 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
> - Issue detail is where operators coordinate review, approvals, and
follow-up work with active runs
> - That thread UI needs to surface blockers, descendants, review
handoffs, and reply ergonomics clearly enough for humans to guide agent
work
> - Several small gaps in the issue-thread flow were making review and
navigation clunkier than necessary
> - This pull request improves the reply composer, descendant/blocker
presentation, interaction folding, and review-request handoff plumbing
together as one cohesive issue-thread workflow slice
> - The benefit is a cleaner operator review loop without changing the
broader task model
## What Changed
- restored and refined the floating reply composer behavior in the issue
thread
- folded expired confirmation interactions and improved post-submit
thread scrolling behavior
- surfaced descendant issue context and inline blocker/paused-assignee
notices on the issue detail view
- tightened large-board first paint behavior in `IssuesList`
- added loose review-request handoffs through the issue
execution-policy/update path and covered them with tests
## Verification
- `pnpm vitest run ui/src/pages/IssueDetail.test.tsx`
- `pnpm vitest run server/src/__tests__/issues-service.test.ts
server/src/__tests__/issue-execution-policy.test.ts`
- `pnpm exec vitest run --project @paperclipai/ui
ui/src/components/IssueChatThread.test.tsx
ui/src/components/IssueProperties.test.tsx
ui/src/components/IssuesList.test.tsx ui/src/lib/issue-tree.test.ts
ui/src/api/issues.test.ts`
- `pnpm exec vitest run --project @paperclipai/adapter-utils
packages/adapter-utils/src/server-utils.test.ts`
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/issue-comment-reopen-routes.test.ts -t "coerces
executor handoff patches into workflow-controlled review wakes|wakes the
return assignee with execution_changes_requested"`
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/issue-execution-policy.test.ts
server/src/__tests__/issues-service.test.ts`
## Visual Evidence
- UI layout changes are covered by the focused issue-thread component
and issue-detail tests listed above. Browser screenshots were not
attachable from this automated greploop environment, so reviewers should
use the running preview for final visual confirmation.
## Risks
- Moderate UI-flow risk: these changes touch the issue detail experience
in multiple spots, so regressions would most likely show up as
thread-layout quirks or incorrect review-handoff behavior
> 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 code execution
in the Codex CLI 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
- [x] If this change affects the UI, I have included before/after
screenshots or documented the visual verification path
- [ ] 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 environments subsystem already models execution environments,
but before this branch there was no end-to-end SSH-backed runtime path
for agents to actually run work against a remote box
> - That meant agents could be configured around environment concepts
without a reliable way to execute adapter sessions remotely, sync
workspace state, and preserve run context across supported adapters
> - We also need environment selection to participate in normal
Paperclip control-plane behavior: agent defaults, project/issue
selection, route validation, and environment probing
> - Because this capability is still experimental, the UI surface should
be easy to hide and easy to remove later without undoing the underlying
implementation
> - This pull request adds SSH environment execution support across the
runtime, adapters, routes, schema, and tests, then puts the visible
environment-management UI behind an experimental flag
> - The benefit is that we can validate real SSH-backed agent execution
now while keeping the user-facing controls safely gated until the
feature is ready to come out of experimentation
## What Changed
- Added SSH-backed execution target support in the shared adapter
runtime, including remote workspace preparation, skill/runtime asset
sync, remote session handling, and workspace restore behavior after
runs.
- Added SSH execution coverage for supported local adapters, plus remote
execution tests across Claude, Codex, Cursor, Gemini, OpenCode, and Pi.
- Added environment selection and environment-management backend support
needed for SSH execution, including route/service work, validation,
probing, and agent default environment persistence.
- Added CLI support for SSH environment lab verification and updated
related docs/tests.
- Added the `enableEnvironments` experimental flag and gated the
environment UI behind it on company settings, agent configuration, and
project configuration surfaces.
## Verification
- `pnpm exec vitest run
packages/adapters/claude-local/src/server/execute.remote.test.ts
packages/adapters/cursor-local/src/server/execute.remote.test.ts
packages/adapters/gemini-local/src/server/execute.remote.test.ts
packages/adapters/opencode-local/src/server/execute.remote.test.ts
packages/adapters/pi-local/src/server/execute.remote.test.ts`
- `pnpm exec vitest run server/src/__tests__/environment-routes.test.ts`
- `pnpm exec vitest run
server/src/__tests__/instance-settings-routes.test.ts`
- `pnpm exec vitest run ui/src/lib/new-agent-hire-payload.test.ts
ui/src/lib/new-agent-runtime-config.test.ts`
- `pnpm -r typecheck`
- `pnpm build`
- Manual verification on a branch-local dev server:
- enabled the experimental flag
- created an SSH environment
- created a Linux Claude agent using that environment
- confirmed a run executed on the Linux box and synced workspace changes
back
## Risks
- Medium: this touches runtime execution flow across multiple adapters,
so regressions would likely show up in remote session setup, workspace
sync, or environment selection precedence.
- The UI flag reduces exposure, but the underlying runtime and route
changes are still substantial and rely on migration correctness.
- The change set is broad across adapters, control-plane services,
migrations, and UI gating, so review should pay close attention to
environment-selection precedence and remote workspace lifecycle
behavior.
## Model Used
- OpenAI Codex via Paperclip's local Codex adapter, GPT-5-class coding
model with tool use and code execution in the local repo workspace. The
local adapter does not surface a more specific public model version
string in this branch workflow.
## 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 orchestrates AI agents for zero-human companies.
> - This branch extends the issue control-plane so board operators can
pause, cancel, and later restore whole issue subtrees while keeping
descendant execution and wake behavior coherent.
> - That required new hold state in the database, shared contracts,
server routes/services, and issue detail UI controls so subtree actions
are durable and auditable instead of ad hoc.
> - While this branch was in flight, `master` advanced with new
environment lifecycle work, including a new `0065_environments`
migration.
> - Before opening the PR, this branch had to be rebased onto
`paperclipai/paperclip:master` without losing the existing
subtree-control work or leaving conflicting migration numbering behind.
> - This pull request rebases the subtree pause/cancel/restore feature
cleanly onto current `master`, renumbers the hold migration to
`0066_issue_tree_holds`, and preserves the full branch diff in a single
PR.
> - The benefit is that reviewers get one clean, mergeable PR for the
subtree-control feature instead of stale branch history with migration
conflicts.
## What Changed
- Added durable issue subtree hold data structures, shared
API/types/validators, server routes/services, and UI flows for subtree
pause, cancel, and restore operations.
- Added server and UI coverage for subtree previewing, hold
creation/release, dependency-aware scheduling under holds, and issue
detail subtree controls.
- Rebased the branch onto current `paperclipai/paperclip:master` and
renumbered the branch migration from `0065_issue_tree_holds` to
`0066_issue_tree_holds` so it no longer conflicts with upstream
`0065_environments`.
- Added a small follow-up commit that makes restore requests return `200
OK` explicitly while keeping pause/cancel hold creation at `201
Created`, and updated the route test to match that contract.
## Verification
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/shared typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck`
- `cd server && pnpm exec vitest run
src/__tests__/issue-tree-control-routes.test.ts
src/__tests__/issue-tree-control-service.test.ts
src/__tests__/issue-tree-control-service-unit.test.ts
src/__tests__/heartbeat-dependency-scheduling.test.ts`
- `cd ui && pnpm exec vitest run src/components/IssueChatThread.test.tsx
src/pages/IssueDetail.test.tsx`
## Risks
- This is a broad cross-layer change touching DB/schema, shared
contracts, server orchestration, and UI; regressions are most likely
around subtree status restoration or wake suppression/resume edge cases.
- The migration was renumbered during PR prep to avoid the new upstream
`0065_environments` conflict. Reviewers should confirm the final
`0066_issue_tree_holds` ordering is the only hold-related migration that
lands.
- The issue-tree restore endpoint now responds with `200` instead of
relying on implicit behavior, which is semantically better for a restore
operation but still changes an API detail that clients or tests could
have assumed.
> 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 in the Paperclip Codex runtime (GPT-5-class
tool-using coding model; exact deployment ID/context window is not
exposed inside 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
- [ ] If this change affects the UI, I have included before/after
screenshots
- [ ] 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.
> - Operators supervise that work through issues, comments, approvals,
and the board UI.
> - Some agent proposals need structured board/user decisions, not
hidden markdown conventions or heavyweight governed approvals.
> - Issue-thread interactions already provide a natural thread-native
surface for proposed tasks and questions.
> - This pull request extends that surface with request confirmations,
richer interaction cards, and agent/plugin/MCP helpers.
> - The benefit is that plan approvals and yes/no decisions become
explicit, auditable, and resumable without losing the single-issue
workflow.
## What Changed
- Added persisted issue-thread interactions for suggested tasks,
structured questions, and request confirmations.
- Added board UI cards for interaction review, selection, question
answers, and accept/reject confirmation flows.
- Added MCP and plugin SDK helpers for creating interaction cards from
agents/plugins.
- Updated agent wake instructions, onboarding assets, Paperclip skill
docs, and public docs to prefer structured confirmations for
issue-scoped decisions.
- Rebased the branch onto `public-gh/master` and renumbered branch
migrations to `0063` and `0064`; the idempotency migration uses `ADD
COLUMN IF NOT EXISTS` for old branch users.
## Verification
- `git diff --check public-gh/master..HEAD`
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
packages/mcp-server/src/tools.test.ts
packages/shared/src/issue-thread-interactions.test.ts
ui/src/lib/issue-thread-interactions.test.ts
ui/src/lib/issue-chat-messages.test.ts
ui/src/components/IssueThreadInteractionCard.test.tsx
ui/src/components/IssueChatThread.test.tsx
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/services/issue-thread-interactions.test.ts` -> 9 files / 79
tests passed
- `pnpm -r typecheck` -> passed, including `packages/db` migration
numbering check
## Risks
- Medium: this adds a new issue-thread interaction model across
db/shared/server/ui/plugin surfaces.
- Migration risk is reduced by placing this branch after current master
migrations (`0063`, `0064`) and making the idempotency column add
idempotent for users who applied the old branch numbering.
- UI interaction behavior is covered by component tests, but this PR
does not include browser screenshots.
> 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-class coding agent runtime. Exact model ID and
context window are not exposed in this Paperclip run; tool use and local
shell/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 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: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The heartbeat runtime is the control-plane path that turns issue
assignments into agent runs and recovers after process exits.
> - Several edge cases could leave high-volume reads unbounded, stale
runtime services visible, blocked dependency wakes too eager, or
terminal adapter processes still around after output finished.
> - These problems make operator views noisy and make long-running agent
work less predictable.
> - This pull request tightens the runtime/read paths and adds focused
regression coverage.
> - The benefit is safer heartbeat execution and cleaner runtime state
without changing the public task model.
## What Changed
- Bounded high-volume issue/log reads in runtime code paths.
- Hardened heartbeat handling for blocked dependency wakes and terminal
run cleanup.
- Added adapter process cleanup coverage for terminal output cases.
- Added workspace runtime control tests for stale command matching and
stopped services.
## Verification
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
server/src/__tests__/heartbeat-dependency-scheduling.test.ts
ui/src/components/WorkspaceRuntimeControls.test.tsx`
## Risks
- Medium risk because heartbeat cleanup and runtime filtering affect
active agent execution paths.
- No migrations.
> Checked `ROADMAP.md`; this is runtime hardening and bug-fix work, not
a new roadmap-level feature.
## Model Used
- OpenAI Codex, GPT-5-based coding agent, tool-enabled repository
editing 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 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 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>
