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## 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> |
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| 2026-02-16-module-system.md | ||
| 2026-02-18-agent-authentication-implementation.md | ||
| 2026-02-18-agent-authentication.md | ||
| 2026-02-19-agent-mgmt-followup-plan.md | ||
| 2026-02-19-ceo-agent-creation-and-hiring.md | ||
| 2026-02-20-issue-run-orchestration-plan.md | ||
| 2026-02-20-storage-system-implementation.md | ||
| 2026-02-21-humans-and-permissions-implementation.md | ||
| 2026-02-21-humans-and-permissions.md | ||
| 2026-02-23-cursor-cloud-adapter.md | ||
| 2026-02-23-deployment-auth-mode-consolidation.md | ||
| 2026-03-10-workspace-strategy-and-git-worktrees.md | ||
| 2026-03-11-agent-chat-ui-and-issue-backed-conversations.md | ||
| 2026-03-13-agent-evals-framework.md | ||
| 2026-03-13-company-import-export-v2.md | ||
| 2026-03-13-features.md | ||
| 2026-03-13-paperclip-skill-tightening-plan.md | ||
| 2026-03-13-plugin-kitchen-sink-example.md | ||
| 2026-03-13-TOKEN-OPTIMIZATION-PLAN.md | ||
| 2026-03-13-workspace-product-model-and-work-product.md | ||
| 2026-03-14-adapter-skill-sync-rollout.md | ||
| 2026-03-14-billing-ledger-and-reporting.md | ||
| 2026-03-14-budget-policies-and-enforcement.md | ||
| 2026-03-14-skills-ui-product-plan.md | ||
| 2026-03-17-docker-release-browser-e2e.md | ||
| 2026-03-17-memory-service-surface-api.md | ||
| 2026-03-17-release-automation-and-versioning.md | ||
| 2026-04-06-smart-model-routing.md | ||
| 2026-04-06-subissue-creation-on-issue-detail.md | ||
| 2026-04-07-issue-detail-speed-and-optimistic-inventory.md | ||
| 2026-04-07-pi-hooks-survey.md | ||
| 2026-04-08-agent-browser-process-cleanup-plan.md | ||
| 2026-04-08-agent-os-follow-up-plan.md | ||
| 2026-04-08-agent-os-technical-report.md | ||
| 2026-04-12-vscode-task-interoperability-plan.md | ||
| 2026-04-26-plugin-secret-ref-company-scope.md | ||
| 2026-05-06-llm-wiki-paperclip-asset-security-gate.md | ||
| workspace-product-model-and-work-product.md | ||
| workspace-technical-implementation.md | ||