Add knowledgebases

Knowledgebases give bots RAG over documents, scoped like extensions: to
particular bots, to a workspace, or to every bot, with their own button
beside Tools in the composer. Documents are chunked and embedded by the
file-ingest worker with the install's embedding model, which is now an
install-wide setting rather than a per-bot one.

- Word search runs on an FTS5 index ranked by BM25, with a scored LIKE
  fallback for scripts written without spaces.
- Changing the embedding model re-indexes documents automatically.
- Ingest jobs wait without spending attempts while every embedding model
  rests, fail at once on errors retrying can't fix, and keep passages
  searchable by words when the model refuses.
- Settings > Knowledgebases shows each knowledgebase's and document's
  index state: spinner, warning, grey check (words only) or green check.

Co-Authored-By: Claude Opus 5.5 <[email protected]>

AGENTS.md

@@ -174,6 +174,10 @@ Set in Settings > Environment (super admin), not `.env`. `envs` (private; encryp
 - Ingestion: chunks + embeddings into `bot_file_chunks` / `bot_file_vectors` (vec0), worked by `src/file-ingest/`; without an embedding model search falls back to words and says so. sqlite-vec limits: metadata columns are NOT NULL; side-car columns can't be filtered with `MATCH` (filter in code). **Never pass `--vector` to `bunx bun-sqlite schema` in `entrypoint.sh`** (wipes vectors on boot). Changing `AppData.EmbeddingDimensions` needs a manual `--vector` run and a re-ingest.
 - **Foreign keys are off per connection** unless `enableForeignKeys` ran (only `src/server.ts` does). Scripts never fire `ON DELETE CASCADE`, so **any helper that deletes a parent row must delete its children explicitly** (as `deleteBotFile`, `purgeStorage`, `deleteSkill` do). A leftover child fails the next `bun run db:schema` with a foreign key violation.
 
+### Knowledgebases
+
+A fourth extension kind (`ExtensionTables.knowledgebase`): `knowledgebases` given per bot (`bot_knowledgebases`), per workspace (`workspace_knowledgebases`) or every bot (`all_bots`), through the same add/remove/access/default paths as skills (coordinator extension tools leave them out). Documents (`knowledgebase_documents`: an upload in private `media`, paradigm `knowledgebase-document`, or written `content`) are chunked into `knowledgebase_chunks` and embedded into the `knowledgebase_vectors` vec0 table by the file-ingest worker (`file_ingest_queue.document_id`, `ingestKnowledgebaseDocument`), always with the install's embedding model; old passages stay until the new ones are in, `embedding_model` records where vectors came from; whatever can change the install's model (default settings, a provider saved or deleted, the hourly catalog sync) calls `reindexAfterEmbeddingChange`, and Re-index reads a knowledgebase again by hand. Word search runs on `knowledgebase_chunks_fts`, an FTS5 table (`unicode61 remove_diacritics 2`) made by `ensureKnowledgebaseFts` (FTS5 can't be declared in the schema; sync leaves undeclared tables alone), backfilled at boot by `syncKnowledgebaseFts`, ranked by BM25 with a scored `LIKE` fallback for unspaced scripts (`knowledgebaseWordQuery`); every write and delete of `knowledgebase_chunks` updates it. Ingest jobs (`settleFailedIngestJob`) wait without spending an attempt while every embedding model rests, fail at once on an error retrying can't fix, and a document whose model refused keeps its new passages for word search (counted as needing re-index, not failed). Runs get `search_knowledgebase`/`read_knowledgebase_document` (`openBotKnowledgebases`, limited to the run's ones) and replies start with passages found for the unanswered messages (`grabKnowledgebaseContext`); passages are fenced (`knowledgebasePassageBlock`) and `KnowledgebasesNote` says they're never instructions. UI: Settings > Knowledgebases (super admin edits and fills; admins set access), a Knowledgebases group on bot/workspace settings, and the composer's own button beside Tools (`ComposerToolsModal` with `composerKnowledgebasesCopy`). Deleting one deletes its documents' vectors, chunks, media and links explicitly.
+
 ### Files browser (`/admin/files`)
 
 Read-only browser of every volume (`src/utils/storage-volumes.ts`: bots, workspaces, computers, media, mcp, db). `resolveStorageSpec` is the only access gate (members see only their bots' and their own user folders inside a computer, `computerPathAllowed`); `resolveStoragePath` applies the path rules. Links built only by `storageSpecHref`. Deletion stays in the chat's files modal and bot tools.
@@ -184,7 +188,7 @@ Read-only browser of every volume (`src/utils/storage-volumes.ts`: bots, workspa
 - **Providers** (`src/dict/harness-provider-dict.ts`): OpenRouter default plus OpenAI-compatible ones; one adapter today (`src/harness/providers/openai-compatible/`). Keys encrypted in private `harness_providers`, falling back to the preset env.
 - **Catalog:** `harness_models`, synced hourly. OpenRouter "free" means `:free` or `openrouter/free`, never zero prices. Auto picks: `rank-auto-models`.
 - **Calling:** `resolveHarnessCandidates` -> `withCandidates` with process-wide cooldowns; errors are `HarnessError`. Entry points under `text/`, `media/`, `audio/`, `image/`, `embeddings/`. `run-text-loop.ts` sticks to one model, caps steps (`grabHarnessMaxToolSteps`, `grabReplyMaxToolSteps`), trims old tool output to fit context. Models that can't take an image/audio part get it read by vision/transcription first.
-- **Per-bot models:** workspace row > bot row > default; the coordinator always uses the defaults. Every entry point takes `bot_id` and passes it on. Shared form `settings/models/(partials)/harness-settings-form.tsx`.
+- **Per-bot models:** workspace row > bot row > default; the coordinator always uses the defaults. Every entry point takes `bot_id` and passes it on. **Embeddings are install-wide** (`install_wide` in `Harnesses`, `isInstallWideHarness`): `grabHarnessSetting` ignores bot/workspace rows for them, the per-bot/workspace forms don't list them and saving one is refused, so every stored vector comes from one model. Shared form `settings/models/(partials)/harness-settings-form.tsx`.
 - **Tools:** `HarnessTool` built per run; own tools validate with zod. `run-tool-call.ts` reports errors back to the model and caps each call (`AppData.HarnessToolTimeoutMs`). Bot tools in `src/harness/tools/bot/` (memory, instructions, tasks, schedules, `start_task`, coordinator's crew management, `delegate_task` and `hand_over_schedule`, with results relayed back by `relayJobToRequester`).
 - **Extensions:** MCP servers (`mcp_servers`, remote or stdio), custom tools (`custom_tools`: http, script, prompt) and skills (`skills`, runbooks loaded with `load_skill`). Given per bot / per workspace (`botExtensionsSql`); `all_bots` only decides what new bots get. Templates `{{args.x}}`/`{{env.KEY}}` via `fillTemplate`; secrets redacted from results. stdio servers run in a per-process pool. Skill body limits are app settings (`grabSkillBodyMaxChars`, `grabSkillBodyShownChars`). A skill proposal says what it changes (`skillProposalChanges`) to the bot and in the confirm outcome, takes no unknown keys (a misnamed `body` would re-propose the saved runbook) and is refused when it changes nothing.
 - **Bots never add or repoint extensions or set envs.** The coordinator may only change what can't alter where data is sent (name, description, on/off, access). New skills, servers, tools, or changes to a URL, headers, kind, config or a skill's runbook go through `propose_*` -> `extension_proposals` -> `[proposal:ID]` card, which the app describes from the config itself (never from what the bot says) and the super admin confirms (`checkProposalData` re-checks). Stdio servers are never proposed by bots (they run in the app container, which holds the docker socket).
@@ -209,7 +213,7 @@ Read-only browser of every volume (`src/utils/storage-volumes.ts`: bots, workspa
 `AdminSections`: `/admin/bots`, `/admin/workspaces`, `/admin/routines`, `/admin/logs`, `/admin/help`, `/admin/settings`. `/admin` -> `/admin/bots`. Every `/admin/*` page renders in the bots layout (`src/layouts/bots/`); there is no separate admin layout.
 
 - **Rail pages** (`src/dict/rail-pages-dict.ts`): Routines, Files, Usage (crew managers), Activity (`/admin/logs`, super admin), Help (`(data)/help-topics.ts`). Visibility via `canSeeRailItem` for both the popover and the aside.
-- **Settings** (`src/dict/settings-pages-dict.ts`; add a sub page = folder + dict entry): `general` (theme per device, plus super-admin app settings: prompt append, run limits, skill limits; crew-manager storage quota; running version), `profile`, `notifications`, `change-password`, `secrets`, `models`, `environment`, `backups` and `database` (super admin), `bots`, `workspaces`, `computers`, `mcps`, `tools`, `skills` (crew managers), `users` (`canListUsers`).
+- **Settings** (`src/dict/settings-pages-dict.ts`; add a sub page = folder + dict entry): `general` (theme per device, plus super-admin app settings: prompt append, run limits, skill limits; crew-manager storage quota; running version), `profile`, `notifications`, `change-password`, `secrets`, `models`, `environment`, `backups` and `database` (super admin), `bots`, `workspaces`, `computers`, `mcps`, `tools`, `skills`, `knowledgebases` (crew managers), `users` (`canListUsers`).
 - Settings pages use `SettingsShell` (breadcrumbs via `admin-breadcrumbs.tsx`), `SettingsGroup` blocks (no cards) and the sticky `SettingsSaveBar`. Saves don't reload. Keep save notices in component state (`useFormInit` clears `status` on change). Lists share `SettingsList`/`SettingsListRow`/`SettingsRowAction`. Row actions are icon-only (`RowIconButton`).
 - **Backups:** DB snapshots (synchronous) and whole-data archives of `DATA_DIR` into `BACKUP_ARCHIVE_DIR`. Archives and restores outlast a request, so the route only starts the run (`startDataBackupRun`, which holds `with-backup-run-lock.ts`) and the page polls `data-status`. A restore takes a safety archive first, then restarts the process.
 - **Database browser:** strictly read-only; values cut in SQL; state in the address via `databaseHref`.