[codex] Add LLM Wiki plugin package to master (#5716)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system is the extension surface for optional product
capabilities without baking every workflow into core.
> - The LLM Wiki plugin package was reviewed in stacked PR #5592, which
targeted `pap-9173-llm-wiki-rest`.
> - The stack base PR #5597 merged to `master` before #5592 was merged
into that branch, so the plugin package never reached `master`.
> - A direct PR from `pap-9173-llm-wiki-rest` back to `master` would be
noisy because that branch has diverged from current `master`.
> - This pull request reapplies the reviewed
`packages/plugins/plugin-llm-wiki/` package onto current `master` and
updates Docker deps-stage manifest coverage.
> - The branch intentionally no longer changes `pnpm-workspace.yaml`
after maintainer feedback; because the new package is now a root
workspace importer, the remaining integration question is how
maintainers want the root lockfile handled under the current PR policy.

## What Changed

- Added the LLM Wiki plugin package under
`packages/plugins/plugin-llm-wiki/` from the merged PR #5592 head.
- Preserved the post-review cleanup from #5592: generated
design/screenshot artifacts are not committed, and `src/ui/index.tsx` /
`src/wiki.ts` are small public entrypoints.
- Added the new plugin package manifest to the Docker deps stage so
policy can validate package manifest coverage.
- Removed the earlier `pnpm-workspace.yaml` exclusion per maintainer
request, so the plugin is included by the existing `packages/plugins/*`
workspace glob.

## Verification

Current head:
- PGlite migration harness: ran migrations 001-003, verified old
non-space distillation unique constraints were removed, inserted
duplicate cursor and work-item keys in a second space, then reran
migration 003 successfully
- `node ./scripts/check-docker-deps-stage.mjs`
- `git diff --check`

Known current-head install result after removing the workspace
exclusion:
- `pnpm install --frozen-lockfile` fails because `pnpm-lock.yaml` has no
importer for `packages/plugins/plugin-llm-wiki/package.json`.

Previously verified on the same plugin source before the
workspace-exclusion removal:
- `pnpm --filter @paperclipai/plugin-sdk build`
- `cd packages/plugins/plugin-llm-wiki && pnpm install --lockfile=false
&& pnpm test`

## Risks

- The branch now includes `packages/plugins/plugin-llm-wiki` in the root
workspace but does not update `pnpm-lock.yaml`. Root frozen install will
fail until maintainers choose a lockfile path that fits repo policy.
- Committing `pnpm-lock.yaml` directly on this PR conflicts with the
current PR policy check, while excluding the package from
`pnpm-workspace.yaml` was rejected in maintainer feedback.
- The package includes UI code already reviewed in #5592; generated
screenshot/design artifacts were intentionally removed per maintainer
request, so visual review should regenerate screenshots locally if
needed.
- The package depends on plugin host support from #5597, which is
already merged to `master`.

> 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 the targeted checks listed above
- [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

Stack context: #5592 was merged into `pap-9173-llm-wiki-rest` after
#5597 had already merged that branch to `master`, so this follow-up PR
is needed to carry the plugin package itself into `master`.

Co-authored-by: Paperclip <noreply@paperclip.ing>

packages/plugins/plugin-llm-wiki/src/manifest.ts

@@ -0,0 +1,601 @@
+import { readFileSync } from "node:fs";
+import type { PaperclipPluginManifestV1 } from "@paperclipai/plugin-sdk";
+import { DEFAULT_AGENT_INSTRUCTION_FILES, DEFAULT_AGENT_INSTRUCTIONS } from "./templates.js";
+
+export const PLUGIN_ID = "paperclipai.plugin-llm-wiki";
+export const WIKI_ROOT_FOLDER_KEY = "wiki-root";
+export const WIKI_MAINTAINER_AGENT_KEY = "wiki-maintainer";
+export const WIKI_MAINTAINER_SKILL_KEY = "wiki-maintainer";
+export const WIKI_INGEST_SKILL_KEY = "wiki-ingest";
+export const WIKI_QUERY_SKILL_KEY = "wiki-query";
+export const WIKI_LINT_SKILL_KEY = "wiki-lint";
+export const PAPERCLIP_DISTILL_SKILL_KEY = "paperclip-distill";
+export const INDEX_REFRESH_SKILL_KEY = "index-refresh";
+export const WIKI_PROJECT_KEY = "llm-wiki";
+export const CURSOR_WINDOW_ROUTINE_KEY = "cursor-window-processing";
+export const NIGHTLY_LINT_ROUTINE_KEY = "nightly-wiki-lint";
+export const INDEX_REFRESH_ROUTINE_KEY = "index-refresh";
+export const DEFAULT_MAX_SOURCE_BYTES = 250000;
+export const DEFAULT_MAX_PAPERCLIP_ISSUE_SOURCE_CHARS = 12000;
+export const DEFAULT_MAX_PAPERCLIP_CURSOR_WINDOW_CHARS = 60000;
+export const DEFAULT_MAX_PAPERCLIP_ROUTINE_RUN_CHARS = 120000;
+export const DEFAULT_PAPERCLIP_COST_CENTS_PER_1K_CHARS = 1;
+export const WIKI_MAINTENANCE_ROUTINE_KEYS = [
+  CURSOR_WINDOW_ROUTINE_KEY,
+  NIGHTLY_LINT_ROUTINE_KEY,
+  INDEX_REFRESH_ROUTINE_KEY,
+] as const;
+export const WIKI_MANAGED_SKILL_KEYS = [
+  WIKI_MAINTAINER_SKILL_KEY,
+  WIKI_INGEST_SKILL_KEY,
+  WIKI_QUERY_SKILL_KEY,
+  WIKI_LINT_SKILL_KEY,
+  PAPERCLIP_DISTILL_SKILL_KEY,
+  INDEX_REFRESH_SKILL_KEY,
+] as const;
+
+function canonicalSkillKey(skillKey: string) {
+  return `plugin/paperclipai-plugin-llm-wiki/${skillKey}`;
+}
+
+function skillMarkdown(skillKey: (typeof WIKI_MANAGED_SKILL_KEYS)[number]) {
+  return readFileSync(new URL(`../skills/${skillKey}/SKILL.md`, import.meta.url), "utf8");
+}
+
+export const WIKI_MAINTAINER_SKILL_CANONICAL_KEY = canonicalSkillKey(WIKI_MAINTAINER_SKILL_KEY);
+export const WIKI_MANAGED_SKILL_CANONICAL_KEYS = WIKI_MANAGED_SKILL_KEYS.map(canonicalSkillKey);
+
+const CURSOR_WINDOW_ROUTINE_DESCRIPTION = `Process bounded Paperclip issue-history windows into the LLM Wiki.
+
+Run procedure:
+Target space: default (slug: default). Paperclip-derived indexing currently writes only into the default space, so this routine never sweeps other spaces. Per-space Paperclip ingestion profiles are a later phase; until they ship, treat any prompt to operate on a non-default space here as a bug and stop.
+1. Resolve the configured wiki root, then read the default space AGENTS.md, wiki/index.md, and the recent entries in wiki/log.md.
+2. Review recent Paperclip issue, comment, and document activity for non-plugin-operation work. Skip LLM Wiki operation issues so routine output does not feed back into itself.
+3. Synthesize Paperclip project state into wiki/projects/<slug>/standup.md for the executive current-state view, then durable project or root-issue knowledge into focused pages under wiki/projects/<slug>/index.md, wiki/concepts/, or wiki/synthesis/. Keep transient run logs out of durable pages unless they change the project's state or decisions.
+4. Write project material as concept-grouped executive synthesis. Link readable issue identifiers when useful, but do not turn project pages into issue-ID lists, UUID dumps, date ledgers, or metadata reports. Always pass wikiId \`default\` and spaceSlug \`default\` to LLM Wiki tools.
+5. Refresh wiki/index.md and append a short wiki/log.md entry listing the source window, affected pages, skipped windows, warnings, and any follow-up issue needed.
+6. If there is no new durable signal, record that in wiki/log.md and close the routine issue with a concise note.`;
+
+const NIGHTLY_LINT_ROUTINE_DESCRIPTION = `Lint the LLM Wiki for structure, provenance, and stale synthesis.
+
+Run procedure:
+Target space: default (slug: default). Paperclip-derived indexing currently writes only into the default space, so this routine never sweeps other spaces. Per-space Paperclip ingestion profiles are a later phase; until they ship, treat any prompt to operate on a non-default space here as a bug and stop.
+1. Resolve the configured wiki root, then read the default space AGENTS.md, wiki/index.md, wiki/log.md, and the current page list.
+2. Check for orphan pages, missing backlinks, stale source provenance, weak citations, duplicate concepts, contradictory claims, and index/log drift.
+3. Inspect the relevant wiki pages and raw sources before changing content. Do not invent missing provenance.
+4. Apply low-risk fixes directly: refresh backlinks, repair index entries, add missing source links, and append a wiki/log.md lint entry. Always pass wikiId \`default\` and spaceSlug \`default\` to LLM Wiki tools.
+5. For ambiguous contradictions or major rewrites, leave the pages unchanged and create or comment a follow-up Paperclip issue with the exact files and evidence.
+6. Close the routine issue with counts by severity, files changed, and unresolved findings.`;
+
+const INDEX_REFRESH_ROUTINE_DESCRIPTION = `Refresh the LLM Wiki navigation and change log.
+
+Run procedure:
+Target space: default (slug: default). Paperclip-derived indexing currently writes only into the default space, so this routine never sweeps other spaces. Per-space Paperclip ingestion profiles are a later phase; until they ship, treat any prompt to operate on a non-default space here as a bug and stop.
+1. Resolve the configured wiki root, then read the default space AGENTS.md, wiki/index.md, wiki/log.md, and the current page list.
+2. Rebuild wiki/index.md so it lists current wiki pages by category with concise summaries and valid wikilinks, and attaches wiki/projects/<slug>/standup.md links to matching project entries.
+3. Verify recently changed wiki pages and project standups are present in the index and that removed or renamed pages no longer appear.
+4. Do not rewrite content pages unless a broken title or link prevents the index from being accurate. Always pass wikiId \`default\` and spaceSlug \`default\` to LLM Wiki tools.
+5. Append a wiki/log.md entry with the index refresh time, page counts by category, and any unresolved indexing problems.
+6. Close the routine issue with the index changes and any follow-up needed.`;
+
+const manifest: PaperclipPluginManifestV1 = {
+  id: PLUGIN_ID,
+  apiVersion: 1,
+  version: "0.1.0",
+  displayName: "LLM Wiki",
+  description: "Local-file LLM Wiki plugin for source ingestion, wiki browsing, query, lint, and maintenance workflows.",
+  author: "Paperclip",
+  categories: ["automation", "ui"],
+  capabilities: [
+    "events.subscribe",
+    "api.routes.register",
+    "database.namespace.migrate",
+    "database.namespace.read",
+    "database.namespace.write",
+    "companies.read",
+    "projects.read",
+    "projects.managed",
+    "skills.managed",
+    "issues.read",
+    "issue.subtree.read",
+    "issues.create",
+    "issues.update",
+    "issues.wakeup",
+    "issues.orchestration.read",
+    "issue.comments.read",
+    "issue.comments.create",
+    "issue.documents.read",
+    "issue.documents.write",
+    "agents.read",
+    "agents.managed",
+    "agent.sessions.create",
+    "agent.sessions.list",
+    "agent.sessions.send",
+    "agent.sessions.close",
+    "routines.managed",
+    "local.folders",
+    "agent.tools.register",
+    "metrics.write",
+    "activity.log.write",
+    "plugin.state.read",
+    "plugin.state.write",
+    "ui.sidebar.register",
+    "ui.page.register"
+  ],
+  entrypoints: {
+    worker: "./dist/worker.js",
+    ui: "./dist/ui"
+  },
+  database: {
+    namespaceSlug: "llm_wiki",
+    migrationsDir: "migrations",
+    coreReadTables: ["companies", "issues", "projects", "agents"]
+  },
+  localFolders: [
+    {
+      folderKey: WIKI_ROOT_FOLDER_KEY,
+      displayName: "Wiki root",
+      description: "Company-scoped local folder that stores raw sources, wiki pages, Paperclip project standups under wiki/projects/, AGENTS.md, IDEA.md, wiki/index.md, and wiki/log.md.",
+      access: "readWrite",
+      requiredDirectories: [
+        "raw",
+        "wiki",
+        "wiki/sources",
+        "wiki/projects",
+        "wiki/entities",
+        "wiki/concepts",
+        "wiki/synthesis"
+      ],
+      requiredFiles: ["AGENTS.md", "IDEA.md", "wiki/index.md", "wiki/log.md"]
+    }
+  ],
+  agents: [
+    {
+      agentKey: WIKI_MAINTAINER_AGENT_KEY,
+      displayName: "Wiki Maintainer",
+      role: "knowledge-maintainer",
+      title: "LLM Wiki Maintainer",
+      icon: "book-open",
+      capabilities: "Ingests source material, maintains local wiki pages, answers cited questions, and runs wiki lint/maintenance through plugin tools.",
+      adapterType: "claude_local",
+      adapterPreference: ["claude_local", "codex_local", "gemini_local", "opencode_local", "cursor", "pi_local"],
+      adapterConfig: {
+        dangerouslySkipPermissions: false,
+        dangerouslyBypassApprovalsAndSandbox: false,
+        sandbox: true,
+        paperclipSkillSync: {
+          desiredSkills: WIKI_MANAGED_SKILL_CANONICAL_KEYS
+        }
+      },
+      runtimeConfig: {
+        modelProfiles: {
+          cheap: {
+            purpose: "classification, lint planning, index maintenance"
+          }
+        }
+      },
+      permissions: {
+        pluginTools: [PLUGIN_ID]
+      },
+      status: "paused",
+      budgetMonthlyCents: 0,
+      instructions: {
+        entryFile: "AGENTS.md",
+        content: DEFAULT_AGENT_INSTRUCTIONS,
+        files: DEFAULT_AGENT_INSTRUCTION_FILES,
+        assetPath: "agents/wiki-maintainer"
+      }
+    }
+  ],
+  projects: [
+    {
+      projectKey: WIKI_PROJECT_KEY,
+      displayName: "LLM Wiki",
+      description: "Plugin-managed inspection area for LLM Wiki ingest, query, lint, and maintenance operation issues.",
+      status: "in_progress",
+      color: "#2563eb"
+    }
+  ],
+  skills: [
+    {
+      skillKey: WIKI_MAINTAINER_SKILL_KEY,
+      displayName: "LLM Wiki Maintainer",
+      slug: "llm-wiki-maintainer",
+      description: "Use the LLM Wiki plugin tools to maintain a cited local company wiki.",
+      markdown: skillMarkdown(WIKI_MAINTAINER_SKILL_KEY)
+    },
+    {
+      skillKey: WIKI_INGEST_SKILL_KEY,
+      displayName: "Wiki Ingest",
+      slug: WIKI_INGEST_SKILL_KEY,
+      description: "Turn captured raw source material into cited durable LLM Wiki pages.",
+      markdown: skillMarkdown(WIKI_INGEST_SKILL_KEY)
+    },
+    {
+      skillKey: WIKI_QUERY_SKILL_KEY,
+      displayName: "Wiki Query",
+      slug: WIKI_QUERY_SKILL_KEY,
+      description: "Answer questions from the LLM Wiki with citations and optional durable synthesis.",
+      markdown: skillMarkdown(WIKI_QUERY_SKILL_KEY)
+    },
+    {
+      skillKey: WIKI_LINT_SKILL_KEY,
+      displayName: "Wiki Lint",
+      slug: WIKI_LINT_SKILL_KEY,
+      description: "Audit the LLM Wiki for contradictions, orphan pages, weak provenance, broken links, and missing concepts.",
+      markdown: skillMarkdown(WIKI_LINT_SKILL_KEY)
+    },
+    {
+      skillKey: PAPERCLIP_DISTILL_SKILL_KEY,
+      displayName: "Paperclip Distill",
+      slug: PAPERCLIP_DISTILL_SKILL_KEY,
+      description: "Turn Paperclip cursor-window, distill, or backfill source bundles into wiki-insightful project knowledge.",
+      markdown: skillMarkdown(PAPERCLIP_DISTILL_SKILL_KEY)
+    },
+    {
+      skillKey: INDEX_REFRESH_SKILL_KEY,
+      displayName: "Index Refresh",
+      slug: INDEX_REFRESH_SKILL_KEY,
+      description: "Refresh wiki/index.md so it accurately catalogs current wiki pages.",
+      markdown: skillMarkdown(INDEX_REFRESH_SKILL_KEY)
+    }
+  ],
+  routines: [
+    {
+      routineKey: CURSOR_WINDOW_ROUTINE_KEY,
+      title: "Process LLM Wiki updates",
+      description: CURSOR_WINDOW_ROUTINE_DESCRIPTION,
+      status: "paused",
+      priority: "low",
+      assigneeRef: { resourceKind: "agent", resourceKey: WIKI_MAINTAINER_AGENT_KEY },
+      projectRef: { resourceKind: "project", resourceKey: WIKI_PROJECT_KEY },
+      concurrencyPolicy: "skip_if_active",
+      catchUpPolicy: "skip_missed",
+      triggers: [
+        {
+          kind: "schedule",
+          label: "Every 6 hours",
+          enabled: false,
+          cronExpression: "0 */6 * * *",
+          timezone: "UTC",
+          signingMode: null,
+          replayWindowSec: null
+        }
+      ],
+      issueTemplate: {
+        surfaceVisibility: "plugin_operation",
+        originId: "routine:cursor-window-processing",
+        billingCode: "plugin-llm-wiki:distillation"
+      }
+    },
+    {
+      routineKey: NIGHTLY_LINT_ROUTINE_KEY,
+      title: "Run LLM Wiki lint",
+      description: NIGHTLY_LINT_ROUTINE_DESCRIPTION,
+      status: "paused",
+      priority: "low",
+      assigneeRef: { resourceKind: "agent", resourceKey: WIKI_MAINTAINER_AGENT_KEY },
+      projectRef: { resourceKind: "project", resourceKey: WIKI_PROJECT_KEY },
+      concurrencyPolicy: "skip_if_active",
+      catchUpPolicy: "skip_missed",
+      triggers: [
+        {
+          kind: "schedule",
+          label: "Nightly",
+          enabled: false,
+          cronExpression: "0 3 * * *",
+          timezone: "UTC",
+          signingMode: null,
+          replayWindowSec: null
+        }
+      ],
+      issueTemplate: {
+        surfaceVisibility: "plugin_operation",
+        originId: "routine:nightly-wiki-lint",
+        billingCode: "plugin-llm-wiki:maintenance"
+      }
+    },
+    {
+      routineKey: INDEX_REFRESH_ROUTINE_KEY,
+      title: "Refresh LLM Wiki index",
+      description: INDEX_REFRESH_ROUTINE_DESCRIPTION,
+      status: "paused",
+      priority: "low",
+      assigneeRef: { resourceKind: "agent", resourceKey: WIKI_MAINTAINER_AGENT_KEY },
+      projectRef: { resourceKind: "project", resourceKey: WIKI_PROJECT_KEY },
+      concurrencyPolicy: "skip_if_active",
+      catchUpPolicy: "skip_missed",
+      triggers: [
+        {
+          kind: "schedule",
+          label: "Hourly",
+          enabled: false,
+          cronExpression: "0 * * * *",
+          timezone: "UTC",
+          signingMode: null,
+          replayWindowSec: null
+        }
+      ],
+      issueTemplate: {
+        surfaceVisibility: "plugin_operation",
+        originId: "routine:index-refresh",
+        billingCode: "plugin-llm-wiki:maintenance"
+      }
+    }
+  ],
+  tools: [
+    {
+      name: "wiki_search",
+      displayName: "Search Wiki",
+      description: "Search indexed wiki page and source metadata for one wiki space. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          query: { type: "string" },
+          limit: { type: "number" }
+        },
+        required: ["companyId", "wikiId", "query"]
+      }
+    },
+    {
+      name: "wiki_read_page",
+      displayName: "Read Wiki Page",
+      description: "Read a markdown wiki page from one wiki space. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          path: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "path"]
+      }
+    },
+    {
+      name: "wiki_write_page",
+      displayName: "Write Wiki Page",
+      description: "Atomically write a markdown wiki page in one wiki space after plugin path validation and optional hash conflict checks. Operation agents should pass the issue's spaceSlug; omitting it uses the default space. Protected control files such as AGENTS.md and IDEA.md are excluded from agent-tool writes.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          path: { type: "string" },
+          contents: { type: "string" },
+          expectedHash: { type: "string" },
+          summary: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "path", "contents"]
+      }
+    },
+    {
+      name: "wiki_propose_patch",
+      displayName: "Propose Wiki Patch",
+      description: "Return a structured proposed page write for one wiki space without changing files. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          path: { type: "string" },
+          contents: { type: "string" },
+          summary: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "path", "contents"]
+      }
+    },
+    {
+      name: "wiki_list_sources",
+      displayName: "List Wiki Sources",
+      description: "Return captured raw source metadata from one wiki space. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          limit: { type: "number" }
+        },
+        required: ["companyId", "wikiId"]
+      }
+    },
+    {
+      name: "wiki_read_source",
+      displayName: "Read Wiki Source",
+      description: "Read a captured raw source from one wiki space. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          rawPath: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "rawPath"]
+      }
+    },
+    {
+      name: "wiki_append_log",
+      displayName: "Append Wiki Log",
+      description: "Append a maintenance note to one wiki space's wiki/log.md. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          entry: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "entry"]
+      }
+    },
+    {
+      name: "wiki_update_index",
+      displayName: "Update Wiki Index",
+      description: "Atomically replace one wiki space's wiki/index.md with optional hash conflict checks. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          contents: { type: "string" },
+          expectedHash: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "contents"]
+      }
+    },
+    {
+      name: "wiki_list_backlinks",
+      displayName: "List Wiki Backlinks",
+      description: "Return indexed backlinks for a wiki page in one wiki space. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" },
+          path: { type: "string" }
+        },
+        required: ["companyId", "wikiId", "path"]
+      }
+    },
+    {
+      name: "wiki_list_pages",
+      displayName: "List Wiki Pages",
+      description: "Return the known page index from one wiki space's plugin metadata. Operation agents should pass the issue's spaceSlug; omitting it uses the default space.",
+      parametersSchema: {
+        type: "object",
+        properties: {
+          companyId: { type: "string" },
+          wikiId: { type: "string" },
+          spaceSlug: { type: "string" }
+        },
+        required: ["companyId", "wikiId"]
+      }
+    }
+  ],
+  apiRoutes: [
+    {
+      routeKey: "overview",
+      method: "GET",
+      path: "/overview",
+      auth: "board-or-agent",
+      capability: "api.routes.register",
+      companyResolution: { from: "query", key: "companyId" }
+    },
+    {
+      routeKey: "bootstrap",
+      method: "POST",
+      path: "/bootstrap",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "capture-source",
+      method: "POST",
+      path: "/sources",
+      auth: "board-or-agent",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "spaces",
+      method: "GET",
+      path: "/spaces",
+      auth: "board-or-agent",
+      capability: "api.routes.register",
+      companyResolution: { from: "query", key: "companyId" }
+    },
+    {
+      routeKey: "create-space",
+      method: "POST",
+      path: "/spaces",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "update-space",
+      method: "PATCH",
+      path: "/spaces/:spaceSlug",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "bootstrap-space",
+      method: "POST",
+      path: "/spaces/:spaceSlug/bootstrap",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "archive-space",
+      method: "POST",
+      path: "/spaces/:spaceSlug/archive",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "operations",
+      method: "GET",
+      path: "/operations",
+      auth: "board-or-agent",
+      capability: "api.routes.register",
+      companyResolution: { from: "query", key: "companyId" }
+    },
+    {
+      routeKey: "start-query",
+      method: "POST",
+      path: "/query-sessions",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    },
+    {
+      routeKey: "file-as-page",
+      method: "POST",
+      path: "/file-as-page",
+      auth: "board",
+      capability: "api.routes.register",
+      companyResolution: { from: "body", key: "companyId" }
+    }
+  ],
+  ui: {
+    slots: [
+      {
+        type: "sidebar",
+        id: "wiki-sidebar",
+        displayName: "Wiki",
+        exportName: "SidebarLink",
+        order: 35
+      },
+      {
+        type: "page",
+        id: "wiki-page",
+        displayName: "Wiki",
+        exportName: "WikiPage",
+        routePath: "wiki"
+      },
+      {
+        type: "routeSidebar",
+        id: "wiki-route-sidebar",
+        displayName: "Wiki",
+        exportName: "WikiRouteSidebar",
+        routePath: "wiki"
+      }
+    ]
+  }
+};
+
+export default manifest;

packages/plugins/plugin-llm-wiki/src/templates.ts

@@ -0,0 +1,73 @@
+import { readdirSync, readFileSync, statSync } from "node:fs";
+
+export const REQUIRED_WIKI_DIRECTORIES = [
+  "raw",
+  "wiki",
+  "wiki/sources",
+  "wiki/projects",
+  "wiki/entities",
+  "wiki/concepts",
+  "wiki/synthesis",
+] as const;
+
+export const REQUIRED_WIKI_FILES = ["AGENTS.md", "IDEA.md", "wiki/index.md", "wiki/log.md"] as const;
+export const KARPATHY_LLM_WIKI_GIST_URL = "https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f";
+
+function templateFile(path: string): string {
+  return readFileSync(new URL(`../templates/${path}`, import.meta.url), "utf8");
+}
+
+function agentInstructionFiles(agentKey: string): Record<string, string> {
+  const root = new URL(`../agents/${agentKey}/`, import.meta.url);
+  const files: Record<string, string> = {};
+
+  function walk(relativeDir: string) {
+    const dirUrl = new URL(relativeDir ? `${relativeDir}/` : "./", root);
+    for (const entry of readdirSync(dirUrl)) {
+      if (entry === ".DS_Store") continue;
+      const relativePath = relativeDir ? `${relativeDir}/${entry}` : entry;
+      const entryUrl = new URL(relativePath, root);
+      const stat = statSync(entryUrl);
+      if (stat.isDirectory()) {
+        walk(relativePath);
+      } else if (stat.isFile()) {
+        files[relativePath] = readFileSync(entryUrl, "utf8");
+      }
+    }
+  }
+
+  walk("");
+  return Object.fromEntries(Object.entries(files).sort(([left], [right]) => left.localeCompare(right)));
+}
+
+export const DEFAULT_WIKI_SCHEMA = templateFile("AGENTS.md");
+export const DEFAULT_AGENT_INSTRUCTION_FILES = agentInstructionFiles("wiki-maintainer");
+export const DEFAULT_AGENT_INSTRUCTIONS = DEFAULT_AGENT_INSTRUCTION_FILES["AGENTS.md"] ?? "";
+export const DEFAULT_IDEA = templateFile("IDEA.md");
+export const DEFAULT_INDEX = templateFile("wiki/index.md");
+export const DEFAULT_LOG = templateFile("wiki/log.md");
+export const DEFAULT_GITIGNORE = templateFile(".gitignore");
+
+export const QUERY_PROMPT = `Answer from the LLM Wiki using the installed wiki-query skill.
+
+Read the target space's wiki/index.md first, inspect relevant pages and raw/source references in that same space, cite the wiki page paths and raw source paths used, and say when the wiki does not contain enough evidence. Useful durable synthesis should be filed back into wiki/synthesis/ inside that same space. Always pass the operation issue's wikiId and spaceSlug to LLM Wiki tools.
+`;
+
+export const LINT_PROMPT = `Lint the LLM Wiki using the installed wiki-lint skill.
+
+Audit the target space only for contradictions, stale claims, orphan pages, missing backlinks, weak provenance, and wiki/index.md / wiki/log.md drift. Also look for important concepts mentioned without pages and answers that should have been filed back into wiki/. Return findings grouped by severity with concrete file paths, evidence, and suggested fixes — do not auto-apply edits. Always pass the operation issue's wikiId and spaceSlug to LLM Wiki tools.
+`;
+
+export const BOOTSTRAP_FILES: ReadonlyArray<{ path: string; contents: string }> = [
+  { path: ".gitignore", contents: DEFAULT_GITIGNORE },
+  { path: "AGENTS.md", contents: DEFAULT_WIKI_SCHEMA },
+  { path: "IDEA.md", contents: DEFAULT_IDEA },
+  { path: "wiki/index.md", contents: DEFAULT_INDEX },
+  { path: "wiki/log.md", contents: DEFAULT_LOG },
+  { path: "raw/.gitkeep", contents: "" },
+  { path: "wiki/sources/.gitkeep", contents: "" },
+  { path: "wiki/projects/.gitkeep", contents: "" },
+  { path: "wiki/entities/.gitkeep", contents: "" },
+  { path: "wiki/concepts/.gitkeep", contents: "" },
+  { path: "wiki/synthesis/.gitkeep", contents: "" },
+];

packages/plugins/plugin-llm-wiki/src/ui/index.tsx

@@ -0,0 +1 @@
+export { SidebarLink, SettingsPage, WikiPage, WikiRouteSidebar } from "./app.js";

packages/plugins/plugin-llm-wiki/src/ui/issue-attachments.ts

@@ -0,0 +1,49 @@
+type FetchLike = (input: string, init: RequestInit) => Promise<Response>;
+
+export type IngestSourceActionResult = {
+  operation?: {
+    issue?: {
+      id?: unknown;
+    } | null;
+  } | null;
+};
+
+export function readIngestOperationIssueId(result: unknown): string {
+  const issueId = (result as IngestSourceActionResult | null)?.operation?.issue?.id;
+  if (typeof issueId === "string" && issueId.trim()) return issueId;
+  throw new Error("Ingest operation did not return an issue id; the dropped file could not be attached.");
+}
+
+async function readUploadError(response: Response): Promise<string> {
+  const body = await response.json().catch(() => null);
+  if (body && typeof body === "object") {
+    const error = (body as { error?: unknown; message?: unknown }).error;
+    if (typeof error === "string" && error.trim()) return error;
+    const message = (body as { error?: unknown; message?: unknown }).message;
+    if (typeof message === "string" && message.trim()) return message;
+  }
+  return `Attachment upload failed with HTTP ${response.status}.`;
+}
+
+export async function uploadIssueAttachmentFile(input: {
+  companyId: string;
+  issueId: string;
+  file: File;
+  fetchImpl?: FetchLike;
+}): Promise<unknown> {
+  const fetchImpl = input.fetchImpl ?? fetch;
+  const form = new FormData();
+  form.append("file", input.file);
+  const response = await fetchImpl(
+    `/api/companies/${encodeURIComponent(input.companyId)}/issues/${encodeURIComponent(input.issueId)}/attachments`,
+    {
+      method: "POST",
+      credentials: "include",
+      body: form,
+    },
+  );
+  if (!response.ok) {
+    throw new Error(await readUploadError(response));
+  }
+  return response.json();
+}

packages/plugins/plugin-llm-wiki/src/wiki.ts

@@ -0,0 +1 @@
+export * from "./wiki/core.js";