fix(markdown): MULTI_FRONTMATTER stops at the first non-frontmatter line

Review catch on #3163: the fence-pairing scan walked arbitrarily far past
body prose to find a second ---, and one colon-prefixed prose line
(`Note: …`, `TODO: …`) was enough to reject legitimate content at
import. Issue #2743's spec is leading-only detection that stops at the
first non-frontmatter character — the walk now breaks on the first line
that isn't YAML-shaped (key:, list item, comment, indented continuation,
or blank), so an hrule followed by prose is body content, never a
stacked block. Real stacked blocks (adjacent, blank-separated,
list-valued keys) still reject.

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

src/cli.ts

@@ -365,6 +365,12 @@ async function main() {
     if (def.required && params[key] === undefined) {
       if (queryHasAlt && key === 'query') continue;
       const cliName = op.cliHints?.name || op.name;
+      // #2822: when the missing param is the op's stdin-fed one, the usage
+      // line alone is misleading (the positionals may all be present — the
+      // pipe was just empty). Name the real problem.
+      if (op.cliHints?.stdin === key) {
+        console.error(`Error: required "${key}" is missing — stdin was empty or not piped. Pipe content on stdin or pass --${key.replace(/_/g, '-')}.`);
+      }
       const positional = op.cliHints?.positional || [];
       const usage = positional.map(p => `<${p}>`).join(' ');
       console.error(`Usage: gbrain ${cliName} ${usage}`);
@@ -466,11 +472,6 @@ 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
@@ -766,6 +767,10 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
   const params: Record<string, unknown> = {};
   const positional = op.cliHints?.positional || [];
   let posIdx = 0;
+  // #2822: track which params came from positionals so a later flag that
+  // silently discards one (`gbrain put CONTENT --slug foo` — CONTENT was
+  // parsed as the slug) gets a stderr warning instead of vanishing.
+  const positionallySet = new Set<string>();
 
   for (let i = 0; i < args.length; i++) {
     const arg = args[i];
@@ -783,13 +788,20 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
       if (paramDef?.type === 'boolean') {
         params[key] = true;
       } else if (i + 1 < args.length) {
+        if (positionallySet.has(key) && params[key] !== args[i + 1]) {
+          console.error(`Warning: ${arg} overrides the positional <${key}> value ${JSON.stringify(params[key])}.`);
+        }
         params[key] = args[++i];
         if (paramDef?.type === 'number') params[key] = Number(params[key]);
       }
     } else if (posIdx < positional.length) {
       const key = positional[posIdx++];
       const paramDef = op.params[key];
+      if (params[key] !== undefined && params[key] !== (paramDef?.type === 'number' ? Number(arg) : arg)) {
+        console.error(`Warning: positional <${key}> overrides the earlier --${key.replace(/_/g, '-')} value ${JSON.stringify(params[key])}.`);
+      }
       params[key] = paramDef?.type === 'number' ? Number(arg) : arg;
+      positionallySet.add(key);
     }
   }
 
@@ -801,7 +813,11 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
       console.error(`Error: stdin content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
     }
-    params[op.cliHints.stdin] = stdinContent;
+    // #2822: empty/whitespace-only stdin (cron with no input, broken pipe)
+    // stays UNSET so the required-param check rejects the call instead of
+    // silently writing an empty page (0 chunks, invisible to search and
+    // embed --stale).
+    if (stdinContent.trim().length > 0) params[op.cliHints.stdin] = stdinContent;
   }
 
   return params;
@@ -842,44 +858,6 @@ 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) {

src/commands/lint.ts

@@ -48,6 +48,7 @@ const FRONTMATTER_RULE_NAMES: Record<ParseValidationCode, string> = {
   NESTED_QUOTES: 'frontmatter-nested-quotes',
   NON_STRING_FIELD: 'frontmatter-non-string-field',
   EMPTY_FRONTMATTER: 'frontmatter-empty',
+  MULTI_FRONTMATTER: 'frontmatter-multi',
 };
 
 /** Codes whose lint findings are fixable by `gbrain frontmatter validate --fix`. */

src/core/ai/gateway.ts

@@ -1000,24 +1000,9 @@ 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 = JSON.parse(bodyText);
-    if (!json || typeof json !== 'object') return rebuild(bodyText);
+    const json: any = await resp.clone().json();
+    if (!json || typeof json !== 'object') return resp;
     let modified = false;
     if (Array.isArray(json.data)) {
       for (const item of json.data) {
@@ -1052,19 +1037,22 @@ const voyageCompatFetch = (async (input: RequestInfo | URL, init?: RequestInit)
         : 0;
       modified = true;
     }
-    if (!modified) return rebuild(bodyText);
-    return rebuild(JSON.stringify(json));
+    if (!modified) return resp;
+    return new Response(JSON.stringify(json), {
+      status: resp.status,
+      statusText: resp.statusText,
+      headers: resp.headers,
+    });
   } 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 body is correct in that case. Letting the
+    // to the original response 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, pass the original body through
-    // (rebuilt — resp's body stream is already consumed by text()).
-    return rebuild(bodyText);
+    // If parsing/transformation fails, fall back to the original response.
+    return resp;
   }
 }) as unknown as typeof fetch;
 
@@ -1204,21 +1192,9 @@ 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 = JSON.parse(bodyText);
-    if (!json || typeof json !== 'object') return rebuild(bodyText);
+    const json: any = await resp.clone().json();
+    if (!json || typeof json !== 'object') return resp;
     let modified = false;
     if (Array.isArray(json.results) && !Array.isArray(json.data)) {
       // Layer 2 OOM cap — per-embedding size. ZE returns float[] arrays,
@@ -1252,25 +1228,20 @@ const zeroEntropyCompatFetch = (async (input: RequestInfo | URL, init?: RequestI
       // SDK also expects total_tokens; ZE provides it directly.
       modified = true;
     }
-    if (!modified) return rebuild(bodyText);
-    return rebuild(JSON.stringify(json));
+    if (!modified) return resp;
+    return new Response(JSON.stringify(json), {
+      status: resp.status,
+      statusText: resp.statusText,
+      headers: resp.headers,
+    });
   } 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 rebuild(bodyText);
+    return resp;
   }
 }) 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/import-file.ts

@@ -301,6 +301,17 @@ export async function importFromContent(
   // silently fabricated a duplicate at (default, slug) — causing later
   // bare-slug subqueries (getTags, deleteChunks, etc.) to crash with 21000.
   const sourceId = opts.sourceId;
+  // #2822: reject empty/whitespace-only content before any work happens. An
+  // empty page writes 0 chunks — invisible to search AND to `embed --stale`
+  // (nothing to embed), so the mistake never surfaces. Empty content is
+  // always a caller bug (empty piped stdin, bad shell substitution). Thrown
+  // (not returned) so every wrapper site surfaces the message, matching the
+  // ContentSanityBlockError flow.
+  if (content.trim().length === 0) {
+    throw new Error(
+      `Content for "${slug}" is empty; refusing to write an empty page (0 chunks would be invisible to search and embed --stale).`,
+    );
+  }
   // Reject oversized payloads before any parsing, chunking, or embedding happens.
   // Uses Buffer.byteLength to count UTF-8 bytes the same way disk size would,
   // so the network path behaves identically to the file path.
@@ -314,7 +325,17 @@ export async function importFromContent(
     };
   }
 
-  const parsed = parseMarkdown(content, slug + '.md', { activePack: opts.activePack });
+  const parsed = parseMarkdown(content, slug + '.md', { activePack: opts.activePack, validate: true });
+
+  // #2743: reject stacked frontmatter (the double-put corruption class —
+  // already-serialized markdown re-wrapped in fresh frontmatter). gray-matter
+  // parses only the first block; the second would land verbatim in the body
+  // and poison every subsequent round-trip. Only MULTI_FRONTMATTER rejects
+  // here — the other validation codes keep their lint-only semantics.
+  const multiFm = parsed.errors?.find(e => e.code === 'MULTI_FRONTMATTER');
+  if (multiFm) {
+    throw new Error(`MULTI_FRONTMATTER: ${multiFm.message} (slug "${slug}", line ${multiFm.line})`);
+  }
 
   // v0.42 (#1699 trust boundary): strip gate-owned markers from UNTRUSTED
   // input. parseMarkdown preserves every frontmatter key except type/title/

src/core/markdown.ts

@@ -11,7 +11,8 @@ export type ParseValidationCode =
   | 'NULL_BYTES'
   | 'NESTED_QUOTES'
   | 'NON_STRING_FIELD'
-  | 'EMPTY_FRONTMATTER';
+  | 'EMPTY_FRONTMATTER'
+  | 'MULTI_FRONTMATTER';
 
 export interface ParseValidationError {
   code: ParseValidationCode;
@@ -331,6 +332,50 @@ function collectValidationErrors(
       });
     }
   }
+
+  // 9. MULTI_FRONTMATTER (#2743) — a second ---…--- block right after the
+  //    closing fence is stacked frontmatter (the double-put corruption class:
+  //    already-serialized markdown re-wrapped in fresh frontmatter).
+  //    gray-matter parses only the first block and silently leaves the second
+  //    in the body. Heuristic: first non-empty line after the close is `---`,
+  //    a later `---` closes it, EVERY line between is frontmatter-shaped
+  //    (YAML `key:`, `- ` list item, `#` comment, indented continuation, or
+  //    blank — the issue's "stop at the first non-frontmatter character"
+  //    spec), and at least one is a `key:` line. A lone `---` stays a
+  //    markdown horizontal rule, and an hrule followed by prose — even
+  //    colon-prefixed prose like `Note: …` mixed with plain lines — is body
+  //    content, not a stacked block.
+  let afterClose = closeLine + 1;
+  while (afterClose < lines.length && lines[afterClose].trim().length === 0) afterClose++;
+  if (afterClose < lines.length && lines[afterClose].trim() === '---') {
+    let secondClose = -1;
+    for (let i = afterClose + 1; i < lines.length; i++) {
+      const trimmed = lines[i].trim();
+      if (trimmed === '---') {
+        secondClose = i;
+        break;
+      }
+      const yamlShaped =
+        trimmed.length === 0 ||
+        /^[A-Za-z_][\w-]*\s*:/.test(trimmed) ||
+        trimmed.startsWith('- ') ||
+        trimmed === '-' ||
+        trimmed.startsWith('#') ||
+        /^\s/.test(lines[i]);
+      if (!yamlShaped) break; // first non-frontmatter line → body prose, not a stacked block
+    }
+    if (
+      secondClose > afterClose + 1 &&
+      lines.slice(afterClose + 1, secondClose).some(l => /^\s*[A-Za-z_][\w-]*\s*:/.test(l))
+    ) {
+      errors.push({
+        code: 'MULTI_FRONTMATTER',
+        message:
+          'Stacked frontmatter: a second ---…--- block follows the frontmatter (double-put corruption); merge into a single frontmatter block',
+        line: afterClose + 1,
+      });
+    }
+  }
 }
 
 /**

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, search, code_callers, code_callees,
+ * `source_id` / `all_sources` parameter (query, 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
@@ -1442,24 +1442,13 @@ 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;
-    // #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);
+    const scope = sourceScopeOpts(ctx);
 
     // 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/search/hybrid.ts

@@ -1323,18 +1323,8 @@ export async function hybridSearch(
       if (effectiveModality === 'both' && imageVectorList !== null) {
         vectorLists = [...vectorLists, imageVectorList];
       }
-    } 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)}`,
-      );
+    } catch {
+      // Embedding failure is non-fatal, fall back to keyword-only
     }
   }
 

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

@@ -1,115 +0,0 @@
-/**
- * #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

@@ -98,18 +98,16 @@ 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 the body is read', async () => {
+  test('Layer 1: Content-Length pre-check before resp.clone().json()', 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). #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).
+    // within it (mirroring the voyage cap test pattern).
     const zeFetchStart = src.indexOf('const zeroEntropyCompatFetch');
     expect(zeFetchStart).toBeGreaterThan(0);
-    const block = src.slice(zeFetchStart, zeFetchStart + 9000);
+    const block = src.slice(zeFetchStart, zeFetchStart + 8000);
 
     const preCheckIdx = block.indexOf("resp.headers.get('content-length')");
-    const jsonParseIdx = block.indexOf('const bodyText = await resp.text()');
+    const jsonParseIdx = block.indexOf('await resp.clone().json()');
     expect(preCheckIdx).toBeGreaterThan(0);
     expect(jsonParseIdx).toBeGreaterThan(0);
     // The pre-check MUST appear before the JSON parse — Voyage's lesson

test/cli-args.test.ts

@@ -1,4 +1,8 @@
-import { describe, expect, test } from 'bun:test';
+import { afterEach, describe, expect, test } from 'bun:test';
+import { spawnSync } from 'child_process';
+import { join, resolve } from 'path';
+import { mkdtempSync, rmSync } from 'fs';
+import { tmpdir } from 'os';
 import { parseOpArgs } from '../src/cli.ts';
 import { operationsByName } from '../src/core/operations.ts';
 
@@ -20,5 +24,70 @@ describe('parseOpArgs', () => {
       source_id: 'gstack-code-repo-0e4763c9',
     });
   });
+
+  describe('positional/flag overwrite warning (#2822)', () => {
+    const errors: string[] = [];
+    const origError = console.error;
+    const captureErrors = () => {
+      console.error = (...args: unknown[]) => errors.push(args.join(' '));
+    };
+    afterEach(() => {
+      console.error = origError;
+      errors.length = 0;
+    });
+
+    test('a flag that overwrites a positional value warns to stderr', () => {
+      captureErrors();
+      const params = parseOpArgs(operationsByName.query, ['positional text', '--query', 'flag text']);
+      expect(params.query).toBe('flag text');
+      expect(errors.some(e => e.includes('Warning') && e.includes('--query'))).toBe(true);
+    });
+
+    test('a positional that overwrites an earlier flag value warns to stderr', () => {
+      captureErrors();
+      const params = parseOpArgs(operationsByName.query, ['--query', 'flag text', 'positional text']);
+      expect(params.query).toBe('positional text');
+      expect(errors.some(e => e.includes('Warning') && e.includes('<query>'))).toBe(true);
+    });
+
+    test('no warning when flag and positional agree', () => {
+      captureErrors();
+      parseOpArgs(operationsByName.query, ['same', '--query', 'same']);
+      expect(errors).toEqual([]);
+    });
+  });
 });
 
+describe('gbrain put — empty non-TTY stdin rejects (#2822)', () => {
+  const REPO = resolve(import.meta.dir, '..');
+  const CLI = join(REPO, 'src', 'cli.ts');
+
+  const runPut = (input: string) => {
+    // Isolated HOME so a regression can never write into a real brain.
+    const home = mkdtempSync(join(tmpdir(), 'gbrain-put-empty-'));
+    try {
+      return spawnSync('bun', [CLI, 'put', 'inbox/empty-stdin-test'], {
+        stdio: ['pipe', 'pipe', 'pipe'],
+        input,
+        encoding: 'utf-8',
+        timeout: 60_000,
+        env: { ...process.env, HOME: home, GBRAIN_SKIP_STARTUP_HOOKS: '1' },
+      });
+    } finally {
+      rmSync(home, { recursive: true, force: true });
+    }
+  };
+
+  test('empty stdin exits 1 and names the missing content param', () => {
+    const res = runPut('');
+    expect(res.status).toBe(1);
+    expect(res.stderr).toContain('content');
+    expect(res.stderr).toContain('stdin');
+  }, 90_000);
+
+  test('whitespace-only stdin also exits 1', () => {
+    const res = runPut('   \n\t\n');
+    expect(res.status).toBe(1);
+    expect(res.stderr).toContain('stdin');
+  }, 90_000);
+});

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

@@ -1,61 +0,0 @@
-/**
- * #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

@@ -1,77 +0,0 @@
-/**
- * #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/import-file.test.ts

@@ -708,3 +708,32 @@ body unchanged
     expect(shortCircuited).toBe(true);
   });
 });
+
+describe('importFromContent — empty content guard (#2822)', () => {
+  test('empty string throws instead of writing an invisible 0-chunk page', async () => {
+    const engine = mockEngine();
+    await expect(importFromContent(engine, 'inbox/empty', '', { noEmbed: true })).rejects.toThrow(/empty/i);
+    expect((engine as any)._calls.find((c: any) => c.method === 'putPage')).toBeUndefined();
+  });
+
+  test('whitespace-only content throws', async () => {
+    const engine = mockEngine();
+    await expect(importFromContent(engine, 'inbox/ws', '  \n\t \n', { noEmbed: true })).rejects.toThrow(/empty/i);
+  });
+});
+
+describe('importFromContent — stacked frontmatter rejection (#2743)', () => {
+  test('double-put shaped content (two ---…--- blocks) throws MULTI_FRONTMATTER', async () => {
+    const engine = mockEngine();
+    const md = '---\ntitle: outer\n---\n\n---\ntitle: inner\ntype: concept\n---\n\nreal body';
+    await expect(importFromContent(engine, 'inbox/double', md, { noEmbed: true })).rejects.toThrow(/MULTI_FRONTMATTER/);
+    expect((engine as any)._calls.find((c: any) => c.method === 'putPage')).toBeUndefined();
+  });
+
+  test('normal content with horizontal rules in the body still imports', async () => {
+    const engine = mockEngine();
+    const md = '---\ntitle: ok\ntype: concept\n---\n\nprose before\n\n---\n\nprose after the rule';
+    const result = await importFromContent(engine, 'inbox/hrule', md, { noEmbed: true });
+    expect(result.status).toBe('imported');
+  });
+});

test/markdown-validation.test.ts

@@ -256,6 +256,56 @@ body`;
     });
   });
 
+  describe('MULTI_FRONTMATTER (#2743)', () => {
+    test('stacked frontmatter immediately after the close fence', () => {
+      const md = `${fence}\ntitle: outer\n${fence}\n${fence}\ntitle: inner\ntype: concept\n${fence}\n\nbody`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).toContain('MULTI_FRONTMATTER');
+    });
+
+    test('stacked frontmatter with a blank line between blocks (serializeMarkdown shape)', () => {
+      const md = `${fence}\ntitle: outer\n${fence}\n\n${fence}\ntitle: inner\n${fence}\n\nbody`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).toContain('MULTI_FRONTMATTER');
+    });
+
+    test('horizontal rules in the body are NOT flagged', () => {
+      const md = `${fence}\ntitle: ok\n${fence}\n\nsome prose\n\n${fence}\n\nmore prose\n\n${fence}\n\nend`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).not.toContain('MULTI_FRONTMATTER');
+    });
+
+    test('hrule pair at body start without YAML-shaped lines is NOT flagged', () => {
+      const md = `${fence}\ntitle: ok\n${fence}\n\n${fence}\n\nplain prose between rules\n\n${fence}\n\nend`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).not.toContain('MULTI_FRONTMATTER');
+    });
+
+    test('timeline sentinel form is NOT flagged', () => {
+      const md = `${fence}\ntitle: ok\n${fence}\n\nbody text\n\n${fence}\n\n## Timeline\n- 2024-01-01: thing`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).not.toContain('MULTI_FRONTMATTER');
+    });
+
+    test('body hrule + colon-prefixed prose (`Note: …`) mixed with plain lines is NOT flagged', () => {
+      const md = `${fence}\ntitle: ok\ntype: concept\n${fence}\n\n${fence}\n\nNote: remember to follow up\n\nlots of plain prose here\n\n${fence}\n\nmore prose`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).not.toContain('MULTI_FRONTMATTER');
+    });
+
+    test('fence pairing stops at the first non-frontmatter line (no far-fence pairing across prose)', () => {
+      const md = `${fence}\ntitle: ok\n${fence}\n\n${fence}\n\n${'plain prose line\n'.repeat(40)}TODO: fix the widget\n${'more prose\n'.repeat(40)}${fence}\nend`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).not.toContain('MULTI_FRONTMATTER');
+    });
+
+    test('stacked block with list-valued keys is still flagged', () => {
+      const md = `${fence}\ntitle: outer\n${fence}\n\n${fence}\ntitle: inner\ntags:\n  - a\n  - b\n${fence}\n\nbody`;
+      const parsed = parseMarkdown(md, undefined, { validate: true });
+      expect(parsed.errors!.map(e => e.code)).toContain('MULTI_FRONTMATTER');
+    });
+  });
+
   test('error.line is set for line-bearing errors', () => {
     const md = `${fence}\ntype: concept\n${fence}\n# Heading inline\n\nbody\x00drop`;
     const parsed = parseMarkdown(md, undefined, { validate: true });

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

@@ -1,87 +0,0 @@
-/**
- * #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 the body is read (D10 OOM defense)', async () => {
+  test('Layer 1: Content-Length pre-check fires BEFORE resp.clone().json() (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
@@ -47,10 +47,8 @@ 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 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()');
+    // comment text that mentions `await resp.clone().json()` for context.
+    const jsonParseIdx = inboundBlock.indexOf('const json: any = await resp.clone().json()');
     expect(preCheckIdx).toBeGreaterThan(0);
     expect(jsonParseIdx).toBeGreaterThan(0);
     // The pre-check MUST appear before the JSON parse — otherwise the OOM