fix(search): honor per-call source_id/all_sources in the search op — the #1484 hint's advised retry was silently ignored

The zero-hit CLI hint tells users to retry with --source-id __all__, which
works for `query` (routes through resolveRequestedScope) but the `search`
op had no source_id/all_sources params: the flag parsed into params, nothing
consumed it, and the retry re-ran the same single-source search — an
invisible false negative whose params.source_id also suppressed the hint on
the retry. search now resolves per-call scope through the same canonical
fail-closed resolver as query (local __all__ spans the brain; remote
collapses to the caller's grant; out-of-grant source_id is denied).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

skills/article-enrichment/SKILL.md

@@ -85,10 +85,6 @@ gbrain get media/articles/<slug>
 
 # 5. Cross-link entities
 #    For every person/company mentioned, add a timeline back-link.
-#    Mark NEW pages minted for article subjects the reader only reads ABOUT
-#    (not personal contacts) as reference: `gbrain reference <slug>`
-#    (or reference: true in frontmatter). Exempts them from coverage nudges;
-#    they stay searchable. Default for real contacts: do NOT set it.
 ```
 
 ## Quality bar

skills/book-mirror/SKILL.md

@@ -273,13 +273,6 @@ Cross-link entities mentioned in the analysis:
 - For every person the right column references with a brain page, add a
   back-link from `people/<slug>` to the new `media/books/<slug>-personalized`
   page (per `conventions/quality.md` Iron Law).
-- **Mark book figures as reference entities.** Any NEW person/company page you
-  mint for a figure from the book (an author, a historical figure, a company
-  the book discusses) — someone the reader reads ABOUT but doesn't personally
-  interact with — should be flagged: `gbrain reference <slug>` (or
-  `reference: true` in frontmatter). They stay fully searchable/linkable but
-  are exempt from coverage nudges (timeline/links). Skip this for anyone the
-  reader actually knows. Default for normal contacts: do NOT set it.
 
 ## Quality bar (the bar)
 

skills/conventions/reference-entities.md

@@ -1,62 +0,0 @@
-# Convention: Reference entities (canon figures)
-
-Some person/company pages are people/orgs the user **reads about** but does not
-personally interact with — a book's author, a historical figure, a company an
-article discusses (Andy Grove, Kleiner Perkins, Intel…). They are real
-knowledge, worth a page, but they have **no dated history in the user's own
-life**, so the entity coverage metrics (`timeline_coverage`,
-`entity_link_coverage`) flag them as permanently incomplete with no honest fix.
-
-The `reference: true` frontmatter flag resolves this.
-
-## What it does
-
-- A page with `reference: true` is **exempt from the entity coverage metrics
-  only** (`timeline_coverage`, `entity_link_coverage`, and their onboard
-  nudges).
-- It keeps its real `type` (`person` / `company`), so it stays **fully
-  searchable, enrichable, linkable, and edge-resolvable**. NOTHING about
-  retrieval changes — this is the whole reason it's a flag, not a new `type`.
-- It is **opt-in**. Absent / `false` / anything-but-`true` = a normal entity
-  that DOES count toward coverage. **This is the default — do not set it on real
-  contacts.**
-
-## When to set it
-
-Set `reference: true` when the entity is a figure/org the user reads ABOUT, not
-someone they deal with:
-
-- authors and figures discussed in a book (book-mirror) or article
-  (article-enrichment)
-- historical / canon figures imported as reference knowledge
-- companies named only as examples in source material
-
-Do NOT set it for people the user actually meets, emails, or works with — those
-are normal entities whose missing timeline/links is a real, actionable gap.
-
-## How to set it
-
-```bash
-gbrain reference <slug>            # mark as reference
-gbrain reference <slug> --unset    # back to a normal entity
-```
-
-The command writes the flag to BOTH the markdown frontmatter (durable; survives
-re-ingest / engine rebuild — markdown is the source of truth) AND the engine
-JSONB (so coverage reflects it immediately, no re-sync). It's idempotent. You
-can also hand-edit frontmatter (`reference: true`) and re-ingest.
-
-## Why a flag, not a type
-
-A new `type: reference-person` would drop the page out of every
-`type IN ('person','company')` filter — search, enrichment, whoknows, link
-inference — so you'd lose the figure everywhere, not just the metric. The flag
-narrows the change to exactly the coverage denominators and nothing else.
-
-## Implementation
-
-`src/core/reference-flag.ts` — `referenceExclusionSql(alias?)` is the single
-source of truth for the predicate `(frontmatter->>'reference') IS DISTINCT FROM
-'true'`, ANDed into both numerator and denominator at every coverage site
-(getHealth in both engines, onboard/checks.ts, init-nudge.ts). Backed by the GIN
-index on `pages.frontmatter`.

skills/enrich/SKILL.md

@@ -268,18 +268,6 @@ Active items, pending decisions, things to track.
 - **YYYY-MM-DD** | Event description [Source: ...]
 ```
 
-### Reference entities (canon figures)
-
-If the entity is someone/something the user reads ABOUT but does not personally
-interact with — a book author, a historical figure, a company discussed in an
-article — mark the page as reference: `gbrain reference <slug>` (or
-`reference: true` in frontmatter). Reference pages keep their `person`/`company`
-type and stay fully searchable, enrichable, and linkable; they are only exempt
-from the entity coverage nudges (timeline/links) that don't apply to figures
-with no dated history in the user's own life. **Default: do NOT set it** — real
-people and companies the user deals with are normal entities. Full convention:
-`conventions/reference-entities.md`.
-
 ### Step 7: Cross-reference
 
 - Update company pages from person enrichment (and vice versa)

skills/maintain/SKILL.md

@@ -270,11 +270,6 @@ Populate them periodically or after major imports:
 - `gbrain stats` — verify `link_count > 0` and `timeline_entry_count > 0` after extraction.
 - `gbrain health` — review `link_coverage` and `timeline_coverage` percentages
   on entity pages (person/company). Below 50% means more extraction is needed.
-  Note: pages flagged `reference: true` (canon/reference figures the user only
-  reads about) are EXEMPT from these two metrics — if coverage looks stuck
-  because of book/article-imported figures with no real history, mark them with
-  `gbrain reference <slug>` rather than chasing the percentage. See
-  `conventions/reference-entities.md`.
 
 Available link types (use with `gbrain graph-query --type`):
 `attended`, `works_at`, `invested_in`, `founded`, `advises`, `mentions`, `source`.

src/cli.ts

@@ -54,7 +54,7 @@ export function bigintToStringReplacer(_key: string, value: unknown): unknown {
 }
 
 // CLI-only commands that bypass the operation layer
-export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'reference', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
+export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
 // CLI-only commands whose handlers print their own --help text. These are
 // excluded from the generic short-circuit so detailed per-command and
 // per-subcommand usage stays reachable.
@@ -466,6 +466,11 @@ async function main() {
     const result = JSON.parse(JSON.stringify(rawResult, bigintToStringReplacer));
     const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
+    // #1484 — invisible-miss hint: a bare query/search that hit zero results
+    // on a multi-source brain tells the user (stderr) which source it
+    // actually searched and how to widen the scope.
+    const hint = await sourceScopeHint(op.name, params, ctx.sourceId, engine, result);
+    if (hint) console.error(hint);
   } catch (e: unknown) {
     // v0.42.20.0 (codex D4): on error, set exitCode + return so the `finally`
     // STILL runs (drains every background-work sink + disconnects). A bare
@@ -837,6 +842,44 @@ async function makeContext(engine: BrainEngine, params: Record<string, unknown>)
   };
 }
 
+/**
+ * #1484 — a bare `gbrain query`/`search` silently scopes to the resolved
+ * source (usually 'default'); on a multi-source brain a zero-hit run looks
+ * identical to "the brain doesn't know this" even when the answer lives in
+ * another source. Returns a stderr hint when (a) the op is query/search,
+ * (b) it returned zero results, (c) the caller did NOT scope explicitly
+ * (--source / --source-id / --all-sources), and (d) the brain has >1
+ * registered source. Best-effort: any lookup failure returns null.
+ *
+ * Exported for tests (same import-safety contract as formatResult).
+ */
+export async function sourceScopeHint(
+  opName: string,
+  params: Record<string, unknown>,
+  sourceId: string,
+  engine: BrainEngine,
+  result: unknown,
+): Promise<string | null> {
+  if (opName !== 'query' && opName !== 'search') return null;
+  if (!Array.isArray(result) || result.length > 0) return null;
+  // Explicit scoping (flag tier) = user intent; don't second-guess it.
+  if (params.source || params.source_id || params.all_sources) return null;
+  if (sourceId === '__all__') return null;
+  try {
+    const rows = await engine.executeRaw<{ n: number }>(
+      `SELECT count(*)::int AS n FROM sources`,
+    );
+    const n = Number(rows[0]?.n ?? 0);
+    if (n <= 1) return null;
+    return (
+      `Hint: this brain has ${n} sources; you searched only "${sourceId}". ` +
+      `Retry with --source-id __all__ (all sources) or --source-id <id>.`
+    );
+  } catch {
+    return null; // hint is best-effort; never fail the query over it
+  }
+}
+
 // Exported for tests (same import-safety contract as cliAliases/printOpHelp).
 export function formatResult(opName: string, result: unknown): string {
   switch (opName) {
@@ -1652,11 +1695,6 @@ async function handleCliOnly(command: string, args: string[]) {
         await runFiles(engine, args);
         break;
       }
-      case 'reference': {
-        const { runReference } = await import('./commands/reference.ts');
-        await runReference(engine, args);
-        break;
-      }
       case 'embed': {
         const { runEmbed } = await import('./commands/embed.ts');
         await runEmbed(engine, args);

src/commands/reference.ts

@@ -1,130 +0,0 @@
-// gbrain reference <slug> [--unset] [--brain <dir>] [--json]
-//
-// Mark (or unmark) a page as a reference-only entity. A reference page keeps its
-// real type (person/company) — fully searchable/enrichable/linkable — but is
-// exempt from the entity coverage metrics (timeline_coverage,
-// entity_link_coverage). See src/core/reference-flag.ts for the rationale.
-//
-// Durability: the flag is written to BOTH the markdown frontmatter (source of
-// truth; survives re-ingest / engine rebuild) AND the engine `pages.frontmatter`
-// JSONB (so the metric reflects it immediately, no re-sync needed).
-
-import { existsSync, readFileSync, writeFileSync } from 'node:fs';
-import { isAbsolute, join, resolve } from 'node:path';
-import { setCliExitVerdict } from '../core/cli-force-exit.ts';
-import type { BrainEngine } from '../core/engine.ts';
-import { REFERENCE_FRONTMATTER_KEY } from '../core/reference-flag.ts';
-import { resolveSourceId } from '../core/source-resolver.ts';
-
-/** Insert/replace/remove `reference: true` in a markdown frontmatter block.
- *  Minimal-diff: only the one line changes; key order is otherwise preserved. */
-export function applyReferenceFrontmatter(content: string, on: boolean): string {
-  const keyLine = `${REFERENCE_FRONTMATTER_KEY}: true`;
-  const block = content.match(/^---\n([\s\S]*?)\n---/);
-
-  if (!block) {
-    // No frontmatter. Nothing to remove; if setting, prepend a block.
-    if (!on) return content;
-    return `---\n${keyLine}\n---\n\n${content}`;
-  }
-
-  let fm = block[1];
-  const hasKey = new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$`, 'm').test(fm);
-
-  if (on) {
-    fm = hasKey
-      ? fm.replace(new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$`, 'm'), keyLine)
-      : `${fm}\n${keyLine}`;
-  } else {
-    if (!hasKey) return content;
-    fm = fm.replace(new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$\\n?`, 'm'), '');
-  }
-
-  // Function replacement so YAML chars ($, & …) in fm aren't treated as
-  // replacement patterns.
-  return content.replace(/^---\n[\s\S]*?\n---/, () => `---\n${fm}\n---`);
-}
-
-function parseArgs(args: string[]): { slug?: string; unset: boolean; json: boolean; brain?: string; source?: string } {
-  let slug: string | undefined;
-  let unset = false;
-  let json = false;
-  let brain: string | undefined;
-  let source: string | undefined;
-  for (let i = 0; i < args.length; i++) {
-    const a = args[i];
-    if (a === '--unset') unset = true;
-    else if (a === '--json') json = true;
-    else if (a === '--brain' || a === '--dir') brain = args[++i];
-    else if (a === '--source') source = args[++i];
-    else if (!a.startsWith('--') && !slug) slug = a;
-  }
-  return { slug, unset, json, brain, source };
-}
-
-async function resolveBrainDir(engine: BrainEngine, explicit?: string): Promise<string | null> {
-  if (explicit) return resolve(explicit);
-  const configured = await engine.getConfig('sync.repo_path');
-  if (configured && existsSync(configured)) return resolve(configured);
-  return null;
-}
-
-export async function runReference(engine: BrainEngine, args: string[]): Promise<void> {
-  const { slug, unset, json, brain, source } = parseArgs(args);
-  if (!slug) {
-    console.error('Usage: gbrain reference <slug> [--unset] [--source <id>] [--brain <dir>] [--json]');
-    setCliExitVerdict(2);
-    return;
-  }
-
-  const brainDir = await resolveBrainDir(engine, brain);
-  if (!brainDir) {
-    console.error('reference: could not resolve brain dir. Pass --brain <dir> or set sync.repo_path.');
-    setCliExitVerdict(1);
-    return;
-  }
-
-  const rel = slug.endsWith('.md') ? slug : `${slug}.md`;
-  const filePath = isAbsolute(rel) ? rel : join(brainDir, rel);
-  if (!existsSync(filePath)) {
-    console.error(`reference: page not found on disk: ${filePath}`);
-    setCliExitVerdict(1);
-    return;
-  }
-
-  // 1) Durable: edit the markdown frontmatter.
-  const before = readFileSync(filePath, 'utf8');
-  const after = applyReferenceFrontmatter(before, !unset);
-  const fileChanged = after !== before;
-  if (fileChanged) writeFileSync(filePath, after, 'utf8');
-
-  // 2) Immediate: update the engine frontmatter JSONB so the metric reflects it
-  //    without waiting for a re-sync. Scoped to (source_id, slug) — slug is only
-  //    unique per source, so a bare-slug UPDATE would clobber same-named pages
-  //    in every other source. Resolve the source from the brain dir (tier-4
-  //    local_path match) unless --source / GBRAIN_SOURCE overrides.
-  const cleanSlug = slug.replace(/\.md$/, '');
-  const sourceId = await resolveSourceId(engine, source ?? null, brainDir);
-  if (unset) {
-    await engine.executeRaw(
-      `UPDATE pages SET frontmatter = frontmatter - '${REFERENCE_FRONTMATTER_KEY}' WHERE slug = $1 AND source_id = $2`,
-      [cleanSlug, sourceId],
-    );
-  } else {
-    await engine.executeRaw(
-      `UPDATE pages SET frontmatter = jsonb_set(COALESCE(frontmatter, '{}'::jsonb), '{${REFERENCE_FRONTMATTER_KEY}}', 'true'::jsonb) WHERE slug = $1 AND source_id = $2`,
-      [cleanSlug, sourceId],
-    );
-  }
-
-  const result = { slug: cleanSlug, source_id: sourceId, reference: !unset, file_changed: fileChanged, file: filePath };
-  if (json) {
-    console.log(JSON.stringify(result));
-  } else {
-    const verb = unset ? 'unmarked' : 'marked';
-    console.log(`${verb} ${cleanSlug} as reference=${!unset}${fileChanged ? '' : ' (frontmatter already current)'}`);
-    if (!unset) {
-      console.log('  → exempt from timeline_coverage / entity_link_coverage; still fully searchable & linkable.');
-    }
-  }
-}

src/core/ai/gateway.ts

@@ -1000,9 +1000,24 @@ const voyageCompatFetch = (async (input: RequestInfo | URL, init?: RequestInit)
   // Voyage diverges from OpenAI in two places that break the parser:
   //   - `embedding` is a base64 string (SDK schema expects `number[]`)
   //   - `usage` lacks `prompt_tokens` (SDK schema requires it when usage present)
+  //
+  // #1610: read the body ONCE via text() and JSON.parse it. The pre-fix
+  // `await resp.clone().json()` truncated large bodies on bun < 1.1.27
+  // (oven-sh/bun#6348) — the parse threw, the catch fell back to the raw
+  // response, and multi-chunk pages died with "Invalid JSON response".
+  // Every JSON return path below rebuilds the Response so a stale
+  // Content-Length/Content-Encoding header from the original can't lie
+  // about the rewritten body.
+  const bodyText = await resp.text();
+  const rebuild = (body: string) => {
+    const headers = new Headers(resp.headers);
+    headers.delete('content-length');
+    headers.delete('content-encoding');
+    return new Response(body, { status: resp.status, statusText: resp.statusText, headers });
+  };
   try {
-    const json: any = await resp.clone().json();
-    if (!json || typeof json !== 'object') return resp;
+    const json: any = JSON.parse(bodyText);
+    if (!json || typeof json !== 'object') return rebuild(bodyText);
     let modified = false;
     if (Array.isArray(json.data)) {
       for (const item of json.data) {
@@ -1037,22 +1052,19 @@ const voyageCompatFetch = (async (input: RequestInfo | URL, init?: RequestInit)
         : 0;
       modified = true;
     }
-    if (!modified) return resp;
-    return new Response(JSON.stringify(json), {
-      status: resp.status,
-      statusText: resp.statusText,
-      headers: resp.headers,
-    });
+    if (!modified) return rebuild(bodyText);
+    return rebuild(JSON.stringify(json));
   } catch (err) {
     // OOM-cap throws MUST propagate. The catch is here for "Voyage returned
     // JSON I can't reshape" (parse error, unexpected schema) — falling back
-    // to the original response is correct in that case. Letting the
+    // to the original body is correct in that case. Letting the
     // too-large response through here would defeat the entire purpose of
     // Layer 2 (the per-embedding cap that fires when Content-Length wasn't
     // available to Layer 1).
     if (err instanceof VoyageResponseTooLargeError) throw err;
-    // If parsing/transformation fails, fall back to the original response.
-    return resp;
+    // If parsing/transformation fails, pass the original body through
+    // (rebuilt — resp's body stream is already consumed by text()).
+    return rebuild(bodyText);
   }
 }) as unknown as typeof fetch;
 
@@ -1192,9 +1204,21 @@ const zeroEntropyCompatFetch = (async (input: RequestInfo | URL, init?: RequestI
   // validates. Also map usage.total_tokens → prompt_tokens (SDK requires
   // prompt_tokens when `usage` is present — same divergence Voyage hit at
   // gateway.ts:655).
+  //
+  // #1610: read the body ONCE via text() + JSON.parse — `resp.clone().json()`
+  // truncated large bodies on bun < 1.1.27 (oven-sh/bun#6348), so the parse
+  // threw and the catch fell back to the RAW ZE `{results: ...}` shape, which
+  // the AI SDK schema rejects → "Invalid JSON response" on multi-chunk pages.
+  const bodyText = await resp.text();
+  const rebuild = (body: string) => {
+    const headers = new Headers(resp.headers);
+    headers.delete('content-length');
+    headers.delete('content-encoding');
+    return new Response(body, { status: resp.status, statusText: resp.statusText, headers });
+  };
   try {
-    const json: any = await resp.clone().json();
-    if (!json || typeof json !== 'object') return resp;
+    const json: any = JSON.parse(bodyText);
+    if (!json || typeof json !== 'object') return rebuild(bodyText);
     let modified = false;
     if (Array.isArray(json.results) && !Array.isArray(json.data)) {
       // Layer 2 OOM cap — per-embedding size. ZE returns float[] arrays,
@@ -1228,20 +1252,25 @@ const zeroEntropyCompatFetch = (async (input: RequestInfo | URL, init?: RequestI
       // SDK also expects total_tokens; ZE provides it directly.
       modified = true;
     }
-    if (!modified) return resp;
-    return new Response(JSON.stringify(json), {
-      status: resp.status,
-      statusText: resp.statusText,
-      headers: resp.headers,
-    });
+    if (!modified) return rebuild(bodyText);
+    return rebuild(JSON.stringify(json));
   } catch (err) {
     // OOM-cap throws MUST propagate. Voyage's pattern: instanceof check on
     // its own tagged class. Same here — only rethrow our own cap class.
     if (err instanceof ZeroEntropyResponseTooLargeError) throw err;
-    return resp;
+    return rebuild(bodyText);
   }
 }) as unknown as typeof fetch;
 
+/**
+ * Test-only seams (#1610): the compat shims are module-private closures;
+ * exporting them lets tests drive the response-rewrite paths behaviorally
+ * (truncating clone(), stale Content-Length) without a live provider.
+ * Same pattern as __getShrinkStateForTests.
+ */
+export const __voyageCompatFetchForTests = voyageCompatFetch;
+export const __zeroEntropyCompatFetchForTests = zeroEntropyCompatFetch;
+
 /**
  * Generic asymmetric-embedding shim for openai-compatible recipes that
  * ship no compat fetch of their own (llama-server, litellm, ollama, ...).

src/core/onboard/checks.ts

@@ -18,7 +18,6 @@
 import type { BrainEngine } from '../engine.ts';
 import type { RemediationStep } from '../remediation-step.ts';
 import { makeRemediationStep } from '../remediation-step.ts';
-import { referenceExclusionSql } from '../reference-flag.ts';
 
 /** Shared shape returned by all four checks. */
 export interface OnboardCheckResult {
@@ -121,8 +120,7 @@ export async function checkEntityLinkCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL
-         AND ${referenceExclusionSql()}`,
+         AND deleted_at IS NULL`,
   );
 
   if (totalEntities === 0) {
@@ -146,7 +144,6 @@ export async function checkEntityLinkCoverage(
        SELECT p.id FROM pages p ${sampleClause}
        WHERE p.type IN ('person', 'company', 'organization', 'entity')
          AND p.deleted_at IS NULL
-         AND ${referenceExclusionSql('p')}
          AND EXISTS (SELECT 1 FROM links l WHERE l.to_page_id = p.id)
      ) sub`,
   );
@@ -218,8 +215,7 @@ export async function checkTimelineCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL
-         AND ${referenceExclusionSql()}`,
+         AND deleted_at IS NULL`,
   );
 
   if (totalEntities === 0) {
@@ -241,7 +237,6 @@ export async function checkTimelineCoverage(
        SELECT p.id FROM pages p ${sampleClause}
        WHERE p.type IN ('person', 'company', 'organization', 'entity')
          AND p.deleted_at IS NULL
-         AND ${referenceExclusionSql('p')}
          AND EXISTS (SELECT 1 FROM timeline_entries t WHERE t.page_id = p.id)
      ) sub`,
   );

src/core/onboard/init-nudge.ts

@@ -14,7 +14,6 @@
 // also short-circuits (CI/scripted callers see nothing).
 
 import type { BrainEngine } from '../engine.ts';
-import { referenceExclusionSql } from '../reference-flag.ts';
 
 const NUDGE_BUDGET_MS = 3000;
 
@@ -58,8 +57,7 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
       engine.executeRaw<{ count: string | number }>(
         `SELECT COUNT(*) AS count FROM pages
            WHERE type IN ('person', 'company', 'organization', 'entity')
-             AND deleted_at IS NULL
-             AND ${referenceExclusionSql()}`,
+             AND deleted_at IS NULL`,
         [],
         { signal: controller.signal },
       ),
@@ -67,7 +65,6 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
         `SELECT COUNT(*) AS count FROM pages p
            WHERE p.type IN ('person', 'company', 'organization', 'entity')
              AND p.deleted_at IS NULL
-             AND ${referenceExclusionSql('p')}
              AND EXISTS (SELECT 1 FROM links l WHERE l.to_page_id = p.id)`,
         [],
         { signal: controller.signal },
@@ -76,7 +73,6 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
         `SELECT COUNT(*) AS count FROM pages p
            WHERE p.type IN ('person', 'company', 'organization', 'entity')
              AND p.deleted_at IS NULL
-             AND ${referenceExclusionSql('p')}
              AND EXISTS (SELECT 1 FROM timeline_entries t WHERE t.page_id = p.id)`,
         [],
         { signal: controller.signal },

src/core/operations.ts

@@ -499,7 +499,7 @@ export function linkReadScopeOpts(ctx: OperationContext): { sourceId?: string; s
  * FAIL-CLOSED: anything not strictly `ctx.remote === false` is untrusted.
  *
  * This is the SINGLE resolver for every read op that accepts a per-call
- * `source_id` / `all_sources` parameter (query, code_callers, code_callees,
+ * `source_id` / `all_sources` parameter (query, search, code_callers, code_callees,
  * get_page, search_by_image, code_blast, code_flow). Inlining the `__all__`
  * branch per handler is the bug class that leaked cross-source reads (#1924,
  * #1371): a remote client could pass `source_id: '__all__'` to opt out of its
@@ -1442,13 +1442,24 @@ const search: Operation = {
     limit: { type: 'number', description: 'Max results (default 20)' },
     offset: { type: 'number', description: 'Skip first N results (for pagination)' },
     mode: { type: 'string', description: 'Search mode (conservative|balanced|tokenmax). Local callers only.' },
+    source_id: {
+      type: 'string',
+      description:
+        "Scope search to a single source. Defaults to OperationContext.sourceId. Pass '__all__' to span every source for trusted local callers; for remote callers '__all__' spans only your granted sources.",
+    },
+    all_sources: { type: 'boolean', description: "Span sources (equivalent to source_id=__all__): every source locally, your grant remotely." },
   },
   handler: async (ctx, p) => {
     const startedAt = Date.now();
     const queryText = p.query as string;
     const limit = (p.limit as number) || 20;
     const offset = (p.offset as number) || 0;
-    const scope = sourceScopeOpts(ctx);
+    // #1484 follow-up: route through the canonical fail-closed resolver so
+    // `--source-id __all__` / `all_sources` behave the same as on `query`
+    // (the zero-hit CLI hint advises exactly that retry). Without a per-call
+    // param, `search` silently ignored --source-id — the retry looked like
+    // a genuine miss.
+    const scope = resolveRequestedScope(ctx, p.source_id as string | undefined, p.all_sources === true);
 
     // T4/D5 — per-call mode honored ONLY for trusted/local callers so a remote
     // OAuth client can't escalate to the costly tokenmax bundle. Local + unknown

src/core/pglite-engine.ts

@@ -23,7 +23,6 @@ import { runMigrations } from './migrate.ts';
 import { PGLITE_SCHEMA_SQL, getPGLiteSchema } from './pglite-schema.ts';
 import { DEFAULT_EMBEDDING_MODEL, DEFAULT_EMBEDDING_DIMENSIONS } from './ai/defaults.ts';
 import { DELETE_BATCH_SIZE } from './engine-constants.ts';
-import { referenceExclusionSql } from './reference-flag.ts';
 import { MARKDOWN_CHUNKER_VERSION } from './chunkers/recursive.ts';
 import { acquireLock, releaseLock, type LockHandle } from './pglite-lock.ts';
 import { getFtsLanguage } from './fts-language.ts';
@@ -5203,7 +5202,6 @@ export class PGLiteEngine implements BrainEngine {
     const { rows: [h] } = await this.db.query(`
       WITH entity_pages AS (
         SELECT id, slug FROM pages WHERE type IN ('person', 'company')
-          AND ${referenceExclusionSql()}
       )
       SELECT
         (SELECT count(*) FROM pages) as page_count,

src/core/postgres-engine.ts

@@ -5320,12 +5320,7 @@ export class PostgresEngine implements BrainEngine {
     // is working as intended, not an orphan.
     const [h] = await sql`
       WITH entity_pages AS (
-        -- reference:true pages are exempt from coverage metrics.
-        -- Inlined (postgres.js tagged-template interpolation = bound param,
-        -- not raw SQL); keep in sync with referenceExclusionSql() in
-        -- reference-flag.ts.
         SELECT id, slug FROM pages WHERE type IN ('person', 'company')
-          AND (frontmatter->>'reference') IS DISTINCT FROM 'true'
       )
       SELECT
         (SELECT count(*) FROM pages) as page_count,

src/core/reference-flag.ts

@@ -1,37 +0,0 @@
-// Reference / canon entities.
-//
-// A page with frontmatter `reference: true` is a reference-only entity — a
-// figure or organization imported from a book / article / external source that
-// the user reads ABOUT but does not actively interact with (e.g. Andy Grove,
-// Kleiner Perkins). It keeps its real `type` (`person` / `company`), so it stays
-// fully searchable, enrichable, linkable, and edge-resolvable — NOTHING about
-// retrieval changes.
-//
-// The ONLY behavior it opts out of is the entity *coverage* metrics
-// (`timeline_coverage`, `entity_link_coverage` + their onboard-nudge mirrors).
-// Those metrics nudge "this entity should accumulate dated history / inbound
-// links"; that assumption is right for people you actually deal with and wrong
-// for canon imports, which have no dated events in the user's life. Excluding
-// them keeps the metric honest and actionable instead of permanently red.
-//
-// Opt-in: absent / false / anything-but-true = normal entity (the default).
-// Set via `gbrain reference <slug>` (or hand-edit frontmatter).
-
-export const REFERENCE_FRONTMATTER_KEY = 'reference';
-
-/**
- * SQL predicate (true for NON-reference pages) to AND into entity-coverage
- * denominators AND numerators so the ratio stays consistent. JSONB `->>` yields
- * text; `IS DISTINCT FROM 'true'` treats absent (NULL) and every non-true value
- * as a normal counted entity. Backed by the GIN index on `pages.frontmatter`.
- *
- * @param alias optional table alias (e.g. 'p' for `pages p`); omit for bare `pages`.
- *
- * NOTE: postgres-engine.ts uses a postgres.js tagged template where `${}` is a
- * bound parameter, not raw SQL, so it inlines this predicate literally — keep
- * the two in sync.
- */
-export function referenceExclusionSql(alias = ''): string {
-  const col = alias ? `${alias}.frontmatter` : 'frontmatter';
-  return `(${col}->>'${REFERENCE_FRONTMATTER_KEY}') IS DISTINCT FROM 'true'`;
-}

src/core/search/hybrid.ts

@@ -1323,8 +1323,18 @@ export async function hybridSearch(
       if (effectiveModality === 'both' && imageVectorList !== null) {
         vectorLists = [...vectorLists, imageVectorList];
       }
-    } catch {
-      // Embedding failure is non-fatal, fall back to keyword-only
+    } catch (err) {
+      // Embedding/vector failure is non-fatal — fall back to keyword-only —
+      // but say WHY (#1626): this arm only runs when the embedding provider
+      // probed available, so a throw here is a real failure (embed timeout,
+      // transient pooler error on the searchVector fan-out). Pre-fix the bare
+      // catch made a cross-source `--source __all__` run silently collapse to
+      // keyword-only/"No results" with zero diagnostics.
+      warnOncePerProcess(
+        'hybrid-vector-arm-failed',
+        `[gbrain] vector arm failed (fail-open, keyword-only fallback): ` +
+          `${err instanceof Error ? err.message : String(err)}`,
+      );
     }
   }
 

test/ai/compat-fetch-body-read.serial.test.ts

@@ -0,0 +1,115 @@
+/**
+ * #1610 — Voyage/ZeroEntropy compat shims must read the response body ONCE
+ * via text() instead of `resp.clone().json()`.
+ *
+ * On bun < 1.1.27, Response.clone() truncates large bodies (oven-sh/bun#6348):
+ * the clone().json() parse threw, the shim's catch fell back to the ORIGINAL
+ * response — whose wire shape (ZE `{results: ...}`, Voyage base64 embeddings)
+ * the AI SDK's openai-compatible Zod schema rejects — and multi-chunk pages
+ * failed with "Invalid JSON response".
+ *
+ * These tests simulate the truncating clone() and assert the shims still
+ * return the fully rewritten body. They also pin that the rewritten Response
+ * does NOT carry the original (now stale) Content-Length header, which lied
+ * about the rewritten body's size (gateway.ts previously copied
+ * `headers: resp.headers` verbatim).
+ */
+
+import { afterEach, describe, expect, test } from 'bun:test';
+import {
+  __voyageCompatFetchForTests,
+  __zeroEntropyCompatFetchForTests,
+} from '../../src/core/ai/gateway.ts';
+
+const origFetch = globalThis.fetch;
+afterEach(() => {
+  globalThis.fetch = origFetch;
+});
+
+/** Build a Response whose clone() truncates the body (bun < 1.1.27 behavior). */
+function truncatingCloneResponse(body: string): Response {
+  const headers = {
+    'content-type': 'application/json',
+    // Deliberately stale after any rewrite: the original wire body's length.
+    'content-length': String(Buffer.byteLength(body)),
+  };
+  const resp = new Response(body, { status: 200, headers });
+  (resp as any).clone = () =>
+    new Response(body.slice(0, 32), { status: 200, headers });
+  return resp;
+}
+
+describe('voyageCompatFetch — single body read (#1610)', () => {
+  test('rewrites base64 embeddings even when clone() truncates the body', async () => {
+    const floats = new Float32Array([0.5, 0.25, -1]);
+    const b64 = Buffer.from(floats.buffer).toString('base64');
+    const wireBody = JSON.stringify({
+      object: 'list',
+      data: [{ object: 'embedding', embedding: b64, index: 0 }],
+      model: 'voyage-3',
+      usage: { total_tokens: 7 },
+    });
+    globalThis.fetch = (async () => truncatingCloneResponse(wireBody)) as unknown as typeof fetch;
+
+    const out = await __voyageCompatFetchForTests('https://api.voyageai.com/v1/embeddings', {
+      method: 'POST',
+      body: JSON.stringify({ input: ['hello'], model: 'voyage-3' }),
+      headers: { 'content-type': 'application/json' },
+    });
+
+    const json: any = await out.json();
+    expect(Array.from(json.data[0].embedding)).toEqual([0.5, 0.25, -1]);
+    expect(json.usage.prompt_tokens).toBe(7);
+    // Stale Content-Length from the wire body must not survive the rewrite.
+    expect(out.headers.get('content-length')).toBeNull();
+    expect(out.headers.get('content-encoding')).toBeNull();
+  });
+});
+
+describe('zeroEntropyCompatFetch — single body read (#1610)', () => {
+  test('rewrites {results} → {data} even when clone() truncates the body', async () => {
+    const wireBody = JSON.stringify({
+      results: [{ embedding: [0.1, 0.2] }, { embedding: [0.3, 0.4] }],
+      usage: { total_bytes: 42, total_tokens: 9 },
+    });
+    let fetchedUrl = '';
+    globalThis.fetch = (async (url: string | URL | Request) => {
+      fetchedUrl = String(url);
+      return truncatingCloneResponse(wireBody);
+    }) as unknown as typeof fetch;
+
+    const out = await __zeroEntropyCompatFetchForTests('https://api.zeroentropy.dev/v1/embeddings', {
+      method: 'POST',
+      body: JSON.stringify({ input: ['hello'], model: 'zembed-1' }),
+      headers: { 'content-type': 'application/json' },
+    });
+
+    expect(fetchedUrl.endsWith('/v1/models/embed')).toBe(true);
+    const json: any = await out.json();
+    // The AI SDK schema requires {data: [{embedding, index}]} — the raw ZE
+    // {results} fallback is exactly the pre-fix "Invalid JSON response".
+    expect(json.results).toBeUndefined();
+    expect(json.data).toHaveLength(2);
+    expect(json.data[0]).toEqual({ object: 'embedding', embedding: [0.1, 0.2], index: 0 });
+    expect(json.data[1].index).toBe(1);
+    expect(json.usage.prompt_tokens).toBe(9);
+    expect(out.headers.get('content-length')).toBeNull();
+  });
+
+  test('non-JSON body falls back to the original bytes (rebuilt, still readable)', async () => {
+    const wireBody = 'plain text, not json';
+    globalThis.fetch = (async () =>
+      new Response(wireBody, {
+        status: 200,
+        headers: { 'content-type': 'application/json' },
+      })) as unknown as typeof fetch;
+
+    const out = await __zeroEntropyCompatFetchForTests('https://api.zeroentropy.dev/v1/embeddings', {
+      method: 'POST',
+      body: JSON.stringify({ input: ['hello'] }),
+    });
+    // Body was consumed by the shim's single read; the fallback must
+    // rebuild a readable Response rather than return the drained original.
+    expect(await out.text()).toBe(wireBody);
+  });
+});

test/ai/zeroentropy-compat-fetch.test.ts

@@ -98,16 +98,18 @@ describe('zeroEntropyCompatFetch — OOM caps', () => {
     expect(src).toMatch(/MAX_ZEROENTROPY_RESPONSE_BYTES\s*=\s*256\s*\*\s*1024\s*\*\s*1024/);
   });
 
-  test('Layer 1: Content-Length pre-check before resp.clone().json()', async () => {
+  test('Layer 1: Content-Length pre-check before the body is read', async () => {
     const src = await Bun.file(GATEWAY_PATH).text();
     // Find the zeroEntropyCompatFetch block bounds, then assert ordering
-    // within it (mirroring the voyage cap test pattern).
+    // within it (mirroring the voyage cap test pattern). #1610 moved the
+    // body read from `resp.clone().json()` to a single `resp.text()` (bun
+    // < 1.1.27 truncates clone()d bodies, oven-sh/bun#6348).
     const zeFetchStart = src.indexOf('const zeroEntropyCompatFetch');
     expect(zeFetchStart).toBeGreaterThan(0);
-    const block = src.slice(zeFetchStart, zeFetchStart + 8000);
+    const block = src.slice(zeFetchStart, zeFetchStart + 9000);
 
     const preCheckIdx = block.indexOf("resp.headers.get('content-length')");
-    const jsonParseIdx = block.indexOf('await resp.clone().json()');
+    const jsonParseIdx = block.indexOf('const bodyText = await resp.text()');
     expect(preCheckIdx).toBeGreaterThan(0);
     expect(jsonParseIdx).toBeGreaterThan(0);
     // The pre-check MUST appear before the JSON parse — Voyage's lesson

test/cli-source-scope-hint.test.ts

@@ -0,0 +1,61 @@
+/**
+ * #1484 — invisible-miss hint. A bare `gbrain query` resolves to a single
+ * source (usually 'default'); on a multi-source brain a zero-hit run gave no
+ * signal that the answer might live in another source. sourceScopeHint
+ * returns the stderr hint exactly when: query/search op + zero results +
+ * no explicit scoping param + >1 registered source.
+ */
+
+import { describe, expect, test } from 'bun:test';
+import { sourceScopeHint } from '../src/cli.ts';
+import type { BrainEngine } from '../src/core/engine.ts';
+
+function fakeEngine(sourceCount: number, fail = false): BrainEngine {
+  return {
+    executeRaw: async () => {
+      if (fail) throw new Error('sources table missing');
+      return [{ n: sourceCount }];
+    },
+  } as unknown as BrainEngine;
+}
+
+describe('sourceScopeHint (#1484)', () => {
+  test('fires on a bare zero-hit query against a multi-source brain', async () => {
+    const hint = await sourceScopeHint('query', {}, 'default', fakeEngine(3), []);
+    expect(hint).toContain('3 sources');
+    expect(hint).toContain('"default"');
+    expect(hint).toContain('--source-id __all__');
+  });
+
+  test('fires for search too', async () => {
+    const hint = await sourceScopeHint('search', {}, 'wiki', fakeEngine(2), []);
+    expect(hint).toContain('"wiki"');
+  });
+
+  test('silent when results were found', async () => {
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(3), [{ slug: 'a' }])).toBeNull();
+  });
+
+  test('silent when the caller scoped explicitly', async () => {
+    expect(await sourceScopeHint('query', { source_id: 'wiki' }, 'wiki', fakeEngine(3), [])).toBeNull();
+    expect(await sourceScopeHint('query', { source: 'wiki' }, 'wiki', fakeEngine(3), [])).toBeNull();
+    expect(await sourceScopeHint('query', { all_sources: true }, '__all__', fakeEngine(3), [])).toBeNull();
+  });
+
+  test('silent when the resolved scope is already __all__', async () => {
+    expect(await sourceScopeHint('query', {}, '__all__', fakeEngine(3), [])).toBeNull();
+  });
+
+  test('silent on a single-source brain', async () => {
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(1), [])).toBeNull();
+  });
+
+  test('silent for non-search ops and non-array results', async () => {
+    expect(await sourceScopeHint('get_stats', {}, 'default', fakeEngine(3), [])).toBeNull();
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(3), { rows: [] })).toBeNull();
+  });
+
+  test('best-effort: sources lookup failure returns null, never throws', async () => {
+    expect(await sourceScopeHint('query', {}, 'default', fakeEngine(3, true), [])).toBeNull();
+  });
+});

test/hybrid-vector-arm-warn.serial.test.ts

@@ -0,0 +1,77 @@
+/**
+ * #1626 — hybridSearch's text-vector arm must not fail DARK.
+ *
+ * The arm only runs when the embedding provider probed available, so a throw
+ * inside it (embed timeout, transient pooler error on searchVector) is a real
+ * failure. Pre-fix, a bare `catch {}` swallowed it and the run silently
+ * collapsed to keyword-only — under `--source __all__` on a strained pooler
+ * that read as a non-deterministic "No results". The fix logs the swallowed
+ * reason via warnOncePerProcess while keeping the keyword fallback.
+ */
+
+import { afterAll, beforeAll, describe, expect, test } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { hybridSearch } from '../src/core/search/hybrid.ts';
+import {
+  __setEmbedTransportForTests,
+  configureGateway,
+  resetGateway,
+} from '../src/core/ai/gateway.ts';
+import { _resetWarnOnceForTests } from '../src/core/utils.ts';
+
+let engine: PGLiteEngine;
+const origWarn = console.warn;
+
+beforeAll(async () => {
+  // Pin the gateway to OpenAI with a stub key (put-page-provenance pattern):
+  // embed() runs instantiateEmbedding — which requires OPENAI_API_KEY — BEFORE
+  // the stubbed transport is reached. Without this, a keyless CI environment
+  // throws the config error instead of the transport's, and the assertion on
+  // the swallowed reason fails. The key never leaves the process.
+  configureGateway({
+    embedding_model: 'openai:text-embedding-3-large',
+    embedding_dimensions: 1536,
+    env: { ...process.env, OPENAI_API_KEY: process.env.OPENAI_API_KEY || 'sk-test-stub' },
+  });
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+  await engine.putPage('people/alice-example', {
+    type: 'person',
+    title: 'Alice Example',
+    compiled_truth: 'Alice Example is a test person for the vector-arm warn test.',
+  });
+});
+
+afterAll(async () => {
+  console.warn = origWarn;
+  __setEmbedTransportForTests(null);
+  resetGateway();
+  await engine.disconnect();
+});
+
+describe('hybridSearch vector-arm failure telemetry (#1626)', () => {
+  test('embed failure logs the swallowed reason and falls back to keyword', async () => {
+    _resetWarnOnceForTests();
+    // Installing a transport makes isAvailable('embedding') true (test-seam
+    // fast path), so the vector arm RUNS — and then throws.
+    __setEmbedTransportForTests(() => {
+      throw new Error('pooler exploded mid-fanout');
+    });
+    const warnings: string[] = [];
+    console.warn = (...args: unknown[]) => {
+      warnings.push(args.map(String).join(' '));
+    };
+    try {
+      const results = await hybridSearch(engine, 'alice');
+      // Keyword fallback still returns results — fail-open preserved.
+      expect(results.some((r) => r.slug === 'people/alice-example')).toBe(true);
+    } finally {
+      console.warn = origWarn;
+      __setEmbedTransportForTests(null);
+    }
+    const armWarnings = warnings.filter((w) => w.includes('vector arm failed'));
+    expect(armWarnings).toHaveLength(1);
+    expect(armWarnings[0]).toContain('pooler exploded mid-fanout');
+  });
+});

test/reference-flag.test.ts

@@ -1,154 +0,0 @@
-import { describe, expect, test } from 'bun:test';
-import { referenceExclusionSql, REFERENCE_FRONTMATTER_KEY } from '../src/core/reference-flag.ts';
-import { applyReferenceFrontmatter } from '../src/commands/reference.ts';
-
-describe('referenceExclusionSql', () => {
-  test('bare pages (no alias)', () => {
-    expect(referenceExclusionSql()).toBe(`(frontmatter->>'reference') IS DISTINCT FROM 'true'`);
-  });
-  test('aliased', () => {
-    expect(referenceExclusionSql('p')).toBe(`(p.frontmatter->>'reference') IS DISTINCT FROM 'true'`);
-  });
-  test('key constant', () => {
-    expect(REFERENCE_FRONTMATTER_KEY).toBe('reference');
-  });
-});
-
-describe('applyReferenceFrontmatter', () => {
-  const page = `---\ntitle: Andy Grove\ntype: person\ntags: []\n---\n\n# Andy Grove\n\nBody.`;
-
-  test('adds reference: true to an existing frontmatter block', () => {
-    const out = applyReferenceFrontmatter(page, true);
-    expect(out).toContain('reference: true');
-    expect(out).toContain('type: person');   // other keys preserved
-    expect(out).toContain('# Andy Grove');    // body preserved
-  });
-
-  test('is idempotent — does not duplicate the key', () => {
-    const once = applyReferenceFrontmatter(page, true);
-    const twice = applyReferenceFrontmatter(once, true);
-    expect(twice).toBe(once);
-    expect(twice.match(/reference: true/g)).toHaveLength(1);
-  });
-
-  test('replaces a stale reference: false with true', () => {
-    const off = `---\ntype: person\nreference: false\n---\n\nBody.`;
-    const out = applyReferenceFrontmatter(off, true);
-    expect(out).toContain('reference: true');
-    expect(out).not.toContain('reference: false');
-  });
-
-  test('--unset removes the key', () => {
-    const on = applyReferenceFrontmatter(page, true);
-    const off = applyReferenceFrontmatter(on, false);
-    expect(off).not.toContain('reference:');
-    expect(off).toContain('type: person');
-  });
-
-  test('--unset on a page without the key is a no-op', () => {
-    expect(applyReferenceFrontmatter(page, false)).toBe(page);
-  });
-
-  test('setting on a frontmatter-less page prepends a block', () => {
-    const raw = '# Just a heading\n\nNo frontmatter here.';
-    const out = applyReferenceFrontmatter(raw, true);
-    expect(out.startsWith('---\nreference: true\n---\n')).toBe(true);
-    expect(out).toContain('# Just a heading');
-  });
-
-  test('preserves body containing YAML-special chars', () => {
-    const tricky = `---\ntype: person\n---\n\nText with $& and $1 literals.`;
-    const out = applyReferenceFrontmatter(tricky, true);
-    expect(out).toContain('Text with $& and $1 literals.');
-    expect(out).toContain('reference: true');
-  });
-});
-
-// ── e2e: getHealth exemption + (source_id, slug)-scoped JSONB write ─────────
-
-import { afterAll, beforeAll } from 'bun:test';
-import * as fs from 'node:fs';
-import * as os from 'node:os';
-import * as path from 'node:path';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { runReference } from '../src/commands/reference.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-describe('reference flag e2e (PGLite)', () => {
-  let engine: PGLiteEngine;
-  let brainDir: string;
-
-  beforeAll(async () => {
-    engine = new PGLiteEngine();
-    await engine.connect({ database_url: '' });
-    await engine.initSchema();
-
-    brainDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gbrain-ref-'));
-    fs.mkdirSync(path.join(brainDir, 'people'), { recursive: true });
-    fs.writeFileSync(
-      path.join(brainDir, 'people/andy-grove.md'),
-      '---\ntitle: Andy Grove\ntype: person\n---\n\n# Andy Grove\n',
-      'utf8',
-    );
-
-    await engine.executeRaw(
-      `INSERT INTO sources (id, name, local_path, config, created_at)
-       VALUES ('src-a', 'a', $1, '{}'::jsonb, now()), ('src-b', 'b', NULL, '{}'::jsonb, now())`,
-      [brainDir],
-    );
-    // Same slug in BOTH sources — the write must only touch src-a.
-    await engine.putPage('people/andy-grove', {
-      type: 'person', title: 'Andy Grove', compiled_truth: 'canon figure',
-    }, { sourceId: 'src-a' });
-    await engine.putPage('people/andy-grove', {
-      type: 'person', title: 'Andy Grove', compiled_truth: 'other-source twin',
-    }, { sourceId: 'src-b' });
-    // A normal contact WITH a timeline entry, so coverage has a live numerator.
-    const contact = await engine.putPage('people/alice-example', {
-      type: 'person', title: 'Alice Example', compiled_truth: 'real contact',
-    }, { sourceId: 'src-a' });
-    await engine.executeRaw(
-      `INSERT INTO timeline_entries (page_id, date, summary) VALUES ($1, '2026-01-01', 'met')`,
-      [contact.id],
-    );
-  });
-
-  afterAll(async () => {
-    await engine.disconnect();
-    fs.rmSync(brainDir, { recursive: true, force: true });
-  });
-
-  test('runReference scopes the JSONB write to the resolved (source_id, slug)', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () =>
-      runReference(engine, ['people/andy-grove', '--brain', brainDir]));
-
-    const rows = await engine.executeRaw<{ source_id: string; ref: string | null }>(
-      `SELECT source_id, frontmatter->>'reference' AS ref FROM pages WHERE slug = 'people/andy-grove' ORDER BY source_id`,
-    );
-    expect(rows).toEqual([
-      { source_id: 'src-a', ref: 'true' },
-      { source_id: 'src-b', ref: null },   // twin in the other source untouched
-    ]);
-    // Durable half: frontmatter on disk got the flag too.
-    expect(fs.readFileSync(path.join(brainDir, 'people/andy-grove.md'), 'utf8'))
-      .toContain('reference: true');
-  });
-
-  test('getHealth exempts reference pages from timeline/link coverage', async () => {
-    const health = await engine.getHealth();
-    // 3 person pages; the 2 reference-less twins would drag coverage to 1/3.
-    // With the src-a twin marked reference, denominator = 2 (alice + src-b twin).
-    expect(health.timeline_coverage).toBeCloseTo(0.5);
-  });
-
-  test('unset restores the page to a normal counted entity', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () =>
-      runReference(engine, ['people/andy-grove', '--unset', '--brain', brainDir]));
-    const rows = await engine.executeRaw<{ ref: string | null }>(
-      `SELECT frontmatter->>'reference' AS ref FROM pages WHERE slug = 'people/andy-grove' AND source_id = 'src-a'`,
-    );
-    expect(rows[0].ref).toBeNull();
-    const health = await engine.getHealth();
-    expect(health.timeline_coverage).toBeCloseTo(1 / 3);
-  });
-});

test/search-op-source-scope.test.ts

@@ -0,0 +1,87 @@
+/**
+ * #1484 follow-up — the `search` op must honor per-call `source_id` /
+ * `all_sources` through the canonical fail-closed resolver
+ * (resolveRequestedScope), exactly like `query` does.
+ *
+ * Pre-fix, `search` had no source_id param at all: the zero-hit CLI hint
+ * advised "retry with --source-id __all__", the flag parsed into params,
+ * NOTHING consumed it, and the retry silently re-ran the same single-source
+ * search — an invisible false negative (and the retry's params.source_id
+ * suppressed the hint, so the user got no second warning).
+ */
+
+import { describe, expect, test } from 'bun:test';
+import { operationsByName } from '../src/core/operations.ts';
+import type { OperationContext } from '../src/core/operations.ts';
+import type { BrainEngine } from '../src/core/engine.ts';
+
+const searchOp = operationsByName['search'];
+
+/** Fake engine: keyword-only config so the handler's scope goes straight to
+ *  searchKeyword, where we capture the opts it was called with. */
+function makeCtx(remote: boolean, allowedSources?: string[]) {
+  const captured: { opts?: Record<string, unknown> } = {};
+  const engine = {
+    getConfig: async (key: string) => (key === 'search.mcp_keyword_only' ? 'true' : null),
+    searchKeyword: async (_q: string, opts: Record<string, unknown>) => {
+      captured.opts = opts;
+      return [];
+    },
+  } as unknown as BrainEngine;
+  const ctx = {
+    engine,
+    config: { engine: 'pglite' },
+    logger: { info: () => {}, warn: () => {}, error: () => {} },
+    dryRun: false,
+    remote,
+    sourceId: 'default',
+    ...(allowedSources ? { auth: { allowedSources } } : {}),
+  } as unknown as OperationContext;
+  return { ctx, captured };
+}
+
+describe('search op per-call source scope (#1484 follow-up)', () => {
+  test('op declares source_id + all_sources params (the CLI hint advises them)', () => {
+    expect(searchOp.params.source_id).toBeDefined();
+    expect(searchOp.params.all_sources).toBeDefined();
+  });
+
+  test('default: scopes to ctx.sourceId', async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x' });
+    expect(captured.opts?.sourceId).toBe('default');
+  });
+
+  test("local + source_id '__all__' spans the whole brain (no source filter)", async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x', source_id: '__all__' });
+    expect(captured.opts?.sourceId).toBeUndefined();
+    expect(captured.opts?.sourceIds).toBeUndefined();
+  });
+
+  test('local + all_sources=true spans the whole brain', async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x', all_sources: true });
+    expect(captured.opts?.sourceId).toBeUndefined();
+    expect(captured.opts?.sourceIds).toBeUndefined();
+  });
+
+  test('explicit source_id wins over ctx.sourceId', async () => {
+    const { ctx, captured } = makeCtx(false);
+    await searchOp.handler(ctx, { query: 'x', source_id: 'wiki' });
+    expect(captured.opts?.sourceId).toBe('wiki');
+  });
+
+  test("remote + '__all__' collapses to the caller's grant (fail-closed)", async () => {
+    const { ctx, captured } = makeCtx(true, ['wiki', 'essays']);
+    await searchOp.handler(ctx, { query: 'x', source_id: '__all__' });
+    expect(captured.opts?.sourceIds).toEqual(['wiki', 'essays']);
+  });
+
+  test('remote + out-of-grant source_id is denied', async () => {
+    const { ctx } = makeCtx(true, ['wiki']);
+    await expect(searchOp.handler(ctx, { query: 'x', source_id: 'secrets' })).rejects.toThrow(
+      /outside your granted sources/,
+    );
+  });
+});

test/voyage-response-cap.test.ts

@@ -34,7 +34,7 @@ describe('v0.31.8 — voyage Content-Length pre-check + per-item cap', () => {
     expect(source).toMatch(/MAX_VOYAGE_RESPONSE_BYTES\s*=\s*256\s*\*\s*1024\s*\*\s*1024/);
   });
 
-  test('Layer 1: Content-Length pre-check fires BEFORE resp.clone().json() (D10 OOM defense)', async () => {
+  test('Layer 1: Content-Length pre-check fires BEFORE the body is read (D10 OOM defense)', async () => {
     const source = await Bun.file(new URL('../src/core/ai/gateway.ts', import.meta.url)).text();
     // Anchor relative to the post-fetch handler block. The function declaration
     // contains an OUTBOUND request body section earlier; we want to verify
@@ -47,8 +47,10 @@ describe('v0.31.8 — voyage Content-Length pre-check + per-item cap', () => {
     // doesn't pin to comment text.
     const preCheckIdx = inboundBlock.indexOf("resp.headers.get('content-length')");
     // Use the full lvalue assignment so the match doesn't accidentally hit
-    // comment text that mentions `await resp.clone().json()` for context.
-    const jsonParseIdx = inboundBlock.indexOf('const json: any = await resp.clone().json()');
+    // comment text that mentions the body read for context. (#1610 moved the
+    // read from `resp.clone().json()` to a single `resp.text()` — bun <
+    // 1.1.27 truncates clone()d bodies, oven-sh/bun#6348.)
+    const jsonParseIdx = inboundBlock.indexOf('const bodyText = await resp.text()');
     expect(preCheckIdx).toBeGreaterThan(0);
     expect(jsonParseIdx).toBeGreaterThan(0);
     // The pre-check MUST appear before the JSON parse — otherwise the OOM