## Thinking Path > - Paperclip is the control plane for autonomous AI companies, so agent work needs visible ownership, recovery, and operator controls. > - This local branch had accumulated several related control-plane reliability and operator-experience fixes across recovery actions, watchdog folding, model-profile defaults, mentions, markdown editing, plugin launchers, and small UI polish. > - The branch needed to be converted into a PR against the current `origin/master` without losing dirty work or including lockfile/workflow churn. > - The safest standalone shape is a single rollup PR because the recovery/server/UI files overlap heavily across the local commits and splitting would create avoidable conflicts. > - This pull request replays the local branch onto latest `origin/master`, preserves the uncommitted work as logical commits, and adds a Zod 4 validator compatibility fix found during verification. > - The benefit is that the May 17 local branch can be reviewed and merged as one coherent, conflict-free branch under the 100-file Greptile limit. ## What Changed - Rebased the local May 17 branch work onto current `origin/master` in a dedicated worktree. - Preserved and committed previously dirty changes for recovery retry handling, plugin/sidebar launcher polish, and `.herenow` ignores. - Added recovery-action behavior for returning source issues to `todo` when retrying source-scoped recovery. - Included the existing local recovery/liveness/watchdog fold, Codex cheap-profile, markdown/mention, duplicate-agent, and UI polish commits from the branch. - Normalized shared validator `z.record(...)` schemas to explicit string-key records for Zod 4 compatibility. - Confirmed the PR has no `pnpm-lock.yaml` or `.github/workflows/*` changes and stays below the 100-file Greptile limit. ## Verification - `pnpm install --frozen-lockfile --ignore-scripts` - `npm run install` in `node_modules/.pnpm/sqlite3@5.1.7/node_modules/sqlite3` to build the local native sqlite3 binding after installing with scripts disabled - `pnpm exec vitest run packages/shared/src/validators/issue.test.ts packages/shared/src/project-mentions.test.ts packages/adapter-utils/src/server-utils.test.ts server/src/__tests__/heartbeat-model-profile.test.ts server/src/__tests__/issue-recovery-actions.test.ts server/src/__tests__/issue-agent-mutation-ownership-routes.test.ts server/src/__tests__/heartbeat-active-run-output-watchdog.test.ts server/src/__tests__/plugin-local-folders.test.ts ui/src/components/IssueRecoveryActionCard.test.tsx ui/src/components/Sidebar.test.tsx ui/src/components/SidebarAccountMenu.test.tsx ui/src/components/IssueProperties.test.tsx ui/src/components/MarkdownEditor.test.tsx ui/src/components/MarkdownBody.test.tsx ui/src/lib/duplicate-agent-payload.test.ts ui/src/pages/Routines.test.tsx` - First pass: 13 files passed with 201 passing tests; 3 server files failed before sqlite3 native binding was built. - After rebuilding sqlite3: `server/src/__tests__/heartbeat-model-profile.test.ts`, `server/src/__tests__/issue-recovery-actions.test.ts`, and `server/src/__tests__/heartbeat-active-run-output-watchdog.test.ts` passed/loaded; embedded Postgres tests were skipped by the local host guard. - `pnpm --filter @paperclipai/shared typecheck` - `pnpm --filter @paperclipai/adapter-utils typecheck` - `pnpm --filter @paperclipai/server typecheck` - `pnpm --filter @paperclipai/ui typecheck` ## Risks - Medium risk: this is a broad rollup PR across recovery semantics, server tests, shared validators, and UI surfaces. - Some embedded Postgres tests skipped locally due the host guard, so CI should provide the stronger database-backed signal. - UI changes were covered by component tests, but no browser screenshot was captured in this PR creation pass. - This branch may overlap with existing recovery/liveness PR work; merge this PR independently or restack/close overlapping branches rather than merging duplicate implementations together. > 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, tool-enabled local repository and GitHub workflow, medium reasoning effort. ## 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>
LLM Wiki
Local-file LLM Wiki plugin for source ingestion, wiki browsing, query, lint, and maintenance workflows.
Scope
This package is the standalone home for LLM Wiki behavior. Wiki-specific routes, UI, prompts, tools, local-folder templates, migrations, fixtures, and tests live here rather than in Paperclip core.
The alpha surface includes:
- manifest-declared Wiki page, sidebar entry, and settings page
- trusted local folder declaration for
raw/,wiki/,AGENTS.md,IDEA.md,wiki/index.md, andwiki/log.md - plugin database namespace migration for wiki instances, sources, pages, operations, query sessions, and resource bindings
- managed
Wiki Maintaineragent, managedLLM Wikiproject, and paused managed routines for wiki update processing, lint, and index refresh - plugin-operation issue creation using
surfaceVisibility: "plugin_operation" - local source capture into
raw/with metadata rows in the plugin DB namespace - opt-in company-scoped Paperclip event ingestion controls for issues, comments, and documents; event ingestion is disabled by default and routes captured raw provenance into the default space only
- manual Paperclip project/root issue distillation and bounded backfill actions with explicit work items, operation issues, source caps, and estimated cost recording
- Paperclip-derived distillation (cursor windows, manual
distill-now, backfill) always writes into the default wiki space in Phase 1; non-default spaces remain on manual / raw-file ingest until per-space Paperclip ingestion profiles ship - Paperclip-derived distillation maintains
wiki/projects/<slug>/standup.mdas the executive current-state view for each represented project, alongside durablewiki/projects/<slug>/index.mdknowledge pages - wiki page writes with plugin path validation, atomic local-folder writes, metadata/revision rows, backlink extraction, and optional stale-hash protection
- wiki tools for search/read/write/propose patch/source/log/index/backlinks workflows
Phase 5 Security Gate
Paperclip-derived text ingestion stays limited to issue titles/descriptions, issue comments, and issue documents.
- Issue attachments/assets are metadata-only in Phase 5.
- Issue work products are metadata-only in Phase 5.
- The wiki must not fetch
/api/assets/:id/content, dereference work-producturlfields, or store those capability-bearing links in source bundles/snapshots.
The accepted policy lives in doc/plans/2026-05-06-llm-wiki-paperclip-asset-security-gate.md.
Development
pnpm install
pnpm dev # watch builds
pnpm dev:ui # local dev server with hot-reload events
pnpm test
From the Paperclip repo root:
pnpm --filter @paperclipai/plugin-llm-wiki typecheck
pnpm --filter @paperclipai/plugin-llm-wiki test
pnpm --filter @paperclipai/plugin-llm-wiki build
Alpha Verification
Run these commands from the Paperclip repo root before handing off alpha plugin changes:
pnpm --filter @paperclipai/plugin-llm-wiki typecheck
pnpm --filter @paperclipai/plugin-llm-wiki test
pnpm --filter @paperclipai/plugin-llm-wiki build
The focused Vitest suite covers:
- standalone package boundaries and package-local harness dependencies
- required local folder bootstrap writes
- raw source capture plus ingest metadata persistence
- hidden plugin-operation issue creation for ingest/query/file-as-page workflows
- disabled and enabled Paperclip event ingestion paths
- managed routine declarations, manual distill/backfill work items, source cap handling, and backfill project/date scoping
- atomic page writes, metadata/revision rows, backlinks, and stale-hash refusal
- query session creation, run-id recording, stream event forwarding, and completion updates
- filing a streamed query answer back into the wiki through a hidden operation
Remaining alpha gaps:
- Browser screenshot capture is maintained separately under
tests/screenshots; generatedscreenshots/outputs are local artifacts and are ignored by git. - Host-level plugin install and live agent invocation still need Paperclip server/runtime smoke coverage when preparing a release candidate.
Install Into Paperclip
curl -X POST http://127.0.0.1:3100/api/plugins/install \
-H "Content-Type: application/json" \
-d '{"packageName":"/Users/dotta/paperclip/.paperclip/worktrees/PAP-3179-design-a-llm-wiki-plugin/packages/plugins/plugin-llm-wiki","isLocalPath":true}'
Build Options
pnpm builduses esbuild presets from@paperclipai/plugin-sdk/bundlers.pnpm build:rollupuses rollup presets from the same SDK.
After changing manifest-loaded assets such as skills, agent instructions, or templates, recompile the local plugin before re-enabling it:
pnpm --filter @paperclipai/plugin-llm-wiki build
The package-local dist/ directory is ignored by git, but local Paperclip
installs load the compiled dist/manifest.js and dist/worker.js files at
runtime. If activation failed before the rebuild, re-enable the plugin or
restart the Paperclip dev server so the host imports the fresh bundle.
Local File Layout
<configured-wiki-root>/
AGENTS.md
IDEA.md
.gitignore
raw/
.gitkeep
wiki/
index.md
log.md
sources/
.gitkeep
projects/
.gitkeep
<project-slug>/
index.md
standup.md
decisions.md
history.md
entities/
.gitkeep
concepts/
.gitkeep
synthesis/
.gitkeep
Use the settings page or bootstrap-root action to configure the folder and
write the starter files. The plugin uses Paperclip's local folder API for path
containment, symlink checks, read/write validation, and atomic writes.
Bootstrap preserves existing files rather than overwriting operator edits. The
default first-install skeleton is copied from the vanilla LLM Wiki layout, with
CLAUDE.md renamed to AGENTS.md and Paperclip project overviews, standups,
decisions, and history kept together under wiki/projects/<slug>/.
Managed Agent Instructions
Plugin-managed agent instruction bundles live under:
agents/<agent-key>/AGENTS.md
For this plugin the Wiki Maintainer source bundle is agents/wiki-maintainer/AGENTS.md.
Any additional files in that folder are installed as sibling instruction files
for the managed agent. The settings health check reports drift from these
defaults, and resetting the managed agent asks for confirmation before replacing
customized instructions.