## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system needs host contracts and runtime support before
large plugins can integrate cleanly.
> - The source branch mixed the LLM Wiki package with supporting
host/runtime work, managed plugin skills, root-level storage spaces, and
a bookmarks reference plugin.
> - [PAP-9173](/PAP/issues/PAP-9173) asked for the current branch to be
split by file boundary: plugin package separately from everything else.
> - [PAP-9188](/PAP/issues/PAP-9188) clarified that LLM Wiki may have
plugin-local spaces, but Paperclip core should not reorganize top-level
local storage into spaces.
> - Follow-up review clarified that the bookmarks example should not
ship in this PR either.
> - This pull request contains the
non-`packages/plugins/plugin-llm-wiki/` host/runtime work, keeps runtime
state under the selected Paperclip instance root, and no longer includes
the bookmarks example.
## What Changed
- Added/updated plugin host contracts, SDK types, worker RPC plumbing,
managed plugin skill support, and related server tests.
- Removed the bookmarks example plugin package and its
bundled-example/workspace references.
- Removed the root-level local spaces CLI/migration surface and restored
instance-root runtime defaults for config, db, logs, storage, secrets,
workspaces, projects, and adapter homes.
- Replaced shared root `space-paths` helpers with `home-paths` helpers
for core runtime storage.
- Tightened stranded recovery unique-conflict detection so concurrent
recovery scans reuse the raced recovery issue when Postgres errors are
wrapped.
- Kept `packages/plugins/plugin-llm-wiki/` out of this PR diff;
plugin-local spaces remain in the stacked plugin-only PR.
## Verification
- `pnpm exec vitest run cli/src/__tests__/data-dir.test.ts
cli/src/__tests__/home-paths.test.ts cli/src/__tests__/onboard.test.ts
packages/shared/src/home-paths.test.ts
packages/db/src/runtime-config.test.ts
server/src/__tests__/agent-instructions-service.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts`
- `pnpm exec vitest run packages/db/src/runtime-config.test.ts`
- `pnpm exec vitest run
server/src/__tests__/plugin-routes-authz.test.ts`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "reuses the
raced stranded recovery issue"` skipped locally because embedded
Postgres did not initialize on this macOS temp host; the code path was
typechecked and is covered by Linux CI.
- Boundary check: no core references remain for `PAPERCLIP_SPACE_ID`,
`spaces migrate-default`, `@paperclipai/shared/space-paths`,
`registerSpacesCommands`, or the removed bookmarks example.
- Previous PR head `4f23e034` had green GitHub checks: `verify`, all
four serialized server shards, `e2e`, `Canary Dry Run`, `policy`, Snyk,
and `Greptile Review`. Current head `582f466d` is re-running checks
after the bookmarks deletion.
## Risks
- Plugin host changes touch shared runtime paths, so regressions would
most likely appear in adapter startup, plugin loading, or local dev path
defaults.
- Removing the bookmarks example also removes one demonstration of
plugin database namespaces plus local-folder persistence; remaining
plugin examples still cover bundled example discovery and plugin host
flows.
- The plugin package itself is intentionally deferred to the stacked
plugin-only PR, where LLM Wiki plugin-local spaces live.
- Existing installs that tested the transient root-level spaces CLI
should stop using it; this PR intentionally removes that unsupported
migration surface before merge.
> 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 GPT-5 Codex via Codex CLI, tool use and local code execution
enabled; context window not exposed.
## 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, except where noted above
for host-specific embedded Postgres initialization
- [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
Stacked follow-up: PR #5592 contains only
`packages/plugins/plugin-llm-wiki/` and targets this branch.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI-agent companies and needs secrets handling
to work across local development, hosted operators, and governed agent
execution.
> - The affected subsystem is the company-scoped secrets control plane:
database schema, server services/routes, CLI workflows, and the Secrets
settings UI.
> - The gap was that secrets were local-only and operators could not
manage provider vaults or import existing remote references without
exposing plaintext.
> - This branch adds provider vault configuration plus an AWS Secrets
Manager remote-import path while preserving company boundaries, binding
context, and audit trails.
> - I kept the PR to a single branch PR, removed unrelated
lockfile/package drift, rebased the full branch onto the current
`public-gh/master`, and addressed fresh Greptile findings.
> - The benefit is a reviewable implementation of provider-backed
secrets with focused tests covering provider selection, import
conflicts, deleted secret reuse, rotation guards, and AWS signing
behavior.
## What Changed
- Added provider vault support for company secrets, including provider
config storage, default vault handling, health checks, binding usage,
access events, and remote import preview/commit.
- Added an AWS Secrets Manager provider using SigV4 request signing,
bounded request timeouts, namespace guardrails, cached runtime
credential resolution, and external-reference linking without plaintext
reads.
- Added Secrets UI surfaces for vault management and remote import, plus
CLI/API documentation for setup and operations.
- Stabilized routine webhook secret binding paths and SSH
environment-driver fixture bindings discovered during verification.
- Addressed Greptile and CI findings: no lockfile/package drift,
monotonic migration metadata, disabled-vault default races, soft-deleted
secret hiding/recreate behavior, remove behavior with disabled vaults,
soft-deleted external-reference re-import, non-active rotation guards,
managed-secret soft deletion through PATCH, and per-call AWS SDK
credential client churn.
- Rebased this branch onto `public-gh/master` at `0e1a5828` and
force-pushed with lease to keep this as the single PR for the branch.
## Verification
- `git fetch public-gh master`
- `git rebase public-gh/master`
- `git diff --name-only public-gh/master...HEAD | grep
'^pnpm-lock\.yaml$' || true` confirmed `pnpm-lock.yaml` is not in the PR
diff.
- Confirmed migration ordering: master ends at `0081_optimal_dormammu`;
this PR adds `0082_dry_vision` and
`0083_company_secret_provider_configs`.
- Inspected migrations for repeat safety: new tables/indexes use `IF NOT
EXISTS`; foreign keys are guarded by `DO $$ ... IF NOT EXISTS`; column
additions use `ADD COLUMN IF NOT EXISTS`.
- `pnpm -r typecheck` passed before the Greptile follow-up commits.
- `pnpm test:run` ran the full stable Vitest path before the Greptile
follow-up commits; it completed with 3 timing-related failures under
parallel load: `codex-local-execute.test.ts`,
`cursor-local-execute.test.ts`, and `environment-service.test.ts`.
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/codex-local-execute.test.ts
src/__tests__/cursor-local-execute.test.ts
src/__tests__/environment-service.test.ts` passed on targeted rerun
(`24/24`).
- `pnpm build` passed before the Greptile follow-up commits. Vite
reported existing chunk-size/dynamic-import warnings.
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
exec vitest run src/__tests__/secrets-service.test.ts` passed (`26/26`).
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
exec vitest run src/__tests__/aws-secrets-manager-provider.test.ts
src/__tests__/secrets-service.test.ts` passed (`39/39`).
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
typecheck` passed.
- Captured Storybook screenshots from `ui/storybook-static` for visual
review.
- Latest PR checks on `5ca3a5cf`: `policy`, serialized server suites
1/4-4/4, `Canary Dry Run`, `e2e`, `security/snyk`, and `Greptile Review`
pass; aggregate `verify` is still registering the completed child
checks.
- Greptile review loop continued through the latest requested pass; all
Greptile review threads are resolved and the latest `Greptile Review`
check on `5ca3a5cf` passed with 0 comments added.
## Screenshots
Before: the provider-vault and remote-import surfaces did not exist on
`master`; these are after-state screenshots from the Storybook fixtures.
## Risks
- Migration risk: this adds new secret provider tables and extends
existing secret rows. The migrations were checked for monotonic ordering
and idempotent guards, but reviewers should still inspect upgrade
behavior carefully.
- Provider risk: AWS support uses direct SigV4 requests. Automated tests
cover signing, request timeouts, vault-config selection, namespace
guardrails, pending-version archival, sanitized provider errors, and
service-level cleanup paths. A real-vault AWS smoke test remains
deployment validation for an operator with AWS credentials rather than
an unverified merge blocker in this local branch.
- UI risk: the Secrets page and import dialog are large new surfaces;
screenshots are included above for reviewer inspection.
- Verification risk: the full local stable test command hit
parallel-load timing failures, although the exact failed files passed
when rerun directly.
- Operational risk: remote import intentionally avoids plaintext reads;
operators must understand that imported external references resolve at
runtime and may fail if AWS permissions change.
> 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 coding agent with local shell/tool use in the
Paperclip worktree. Exact context-window size was 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
- [ ] 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>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - Reliable execution depends on heartbeat routing, issue lifecycle
semantics, telemetry, and a fast enough local verification loop to keep
regressions visible
> - The remaining commits on this branch were mostly server/runtime
correctness fixes plus test and documentation follow-ups in that area
> - Those changes are logically separate from the UI-focused
issue-detail and workspace/navigation branches even when they touch
overlapping issue APIs
> - This pull request groups the execution reliability, heartbeat,
telemetry, and tooling changes into one standalone branch
> - The benefit is a focused review of the control-plane correctness
work, including the follow-up fix that restored the implicit
comment-reopen helpers after branch splitting
## What Changed
- Hardened issue/heartbeat execution behavior, including self-review
stage skipping, deferred mention wakes during active execution, stranded
execution recovery, active-run scoping, assignee resolution, and
blocked-to-todo wake resumption
- Reduced noisy polling/logging overhead by trimming issue run payloads,
compacting persisted run logs, silencing high-volume request logs, and
capping heartbeat-run queries in dashboard/inbox surfaces
- Expanded telemetry and status semantics with adapter/model fields on
task completion plus clearer status guidance in docs/onboarding material
- Updated test infrastructure and verification defaults with faster
route-test module isolation, cheaper default `pnpm test`, e2e isolation
from local state, and repo verification follow-ups
- Included docs/release housekeeping from the branch and added a small
follow-up commit restoring the implicit comment-reopen helpers that were
dropped during branch reconstruction
## Verification
- `pnpm vitest run
server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-telemetry-routes.test.ts`
- `pnpm vitest run server/src/__tests__/http-log-policy.test.ts
server/src/__tests__/heartbeat-run-log.test.ts
server/src/__tests__/health.test.ts`
- `server/src/__tests__/activity-service.test.ts`,
`server/src/__tests__/heartbeat-comment-wake-batching.test.ts`, and
`server/src/__tests__/heartbeat-process-recovery.test.ts` were attempted
on this host but the embedded Postgres harness reported
init-script/data-dir problems and skipped or failed to start, so they
are noted as environment-limited
## Risks
- Medium: this branch changes core issue/heartbeat routing and
reopen/wakeup behavior, so regressions would affect agent execution flow
rather than isolated UI polish
- Because it also updates verification infrastructure, reviewers should
pay attention to whether the new tests are asserting the right failure
modes and not just reshaping harness behavior
## Model Used
- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution 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)
- [ ] 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>
* public-gh/master:
Drop lockfile from watcher change
Tighten plugin dev file watching
Fix plugin smoke example typecheck
Fix plugin dev watcher and migration snapshot
Clarify plugin authoring and external dev workflow
Expand kitchen sink plugin demos
fix: set AGENT_HOME env var for agent processes
Add kitchen sink plugin example
Simplify plugin runtime and cleanup lifecycle
Add plugin framework and settings UI
# Conflicts:
# packages/db/src/migrations/meta/0029_snapshot.json
# packages/db/src/migrations/meta/_journal.json
Move plans from doc/plan/ into doc/plans/ and add YYYY-MM-DD date
prefixes to all undated plan files based on document headers or
earliest git commit dates.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Dotta
