docs(tutorial): drop dead --remote flag from company-brain search examples

With unknown op flags now a hard error (this PR), the tutorial's
`gbrain search ... --remote` invocations would fail: no code path ever
read a --remote flag — thin-client installs route shared ops through the
remote MCP server automatically. Update the three examples to the
flagless form and explain the automatic routing.

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

docs/tutorials/company-brain.md

@@ -223,14 +223,16 @@ export GBRAIN_REMOTE_CLIENT_ID=<Alice's client_id>
 export GBRAIN_REMOTE_CLIENT_SECRET=<Alice's client_secret>
 export GBRAIN_REMOTE_MCP_URL=https://brain.acme-co.com/mcp
 
-gbrain search "performance review" --remote
+gbrain search "performance review"
 ```
 
+(On a thin-client install every shared op routes through the remote MCP server automatically — no flag needed. The env vars select whose credentials the call uses.)
+
 Alice should see results only from `customers` and `shared`. The performance-review notes live in `internal`, which she's not scoped to read. She shouldn't see them.
 
 ```bash
 # Terminal 2, as Bob (export his credentials similarly)
-gbrain search "performance review" --remote
+gbrain search "performance review"
 ```
 
 Bob should see the performance-review notes from `internal`, plus anything related from `shared`. He shouldn't see anything that lives only in `customers`.
@@ -514,7 +516,7 @@ The first sync embeds every page, which takes time. Check `gbrain sources status
 
 ### "I see a page I shouldn't see"
 
-This shouldn't happen, but if you suspect it, run `gbrain search <query> --remote --json` as the constrained client and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
+This shouldn't happen, but if you suspect it, run `gbrain search <query> --json` as the constrained client (thin-client install, with the client's `GBRAIN_REMOTE_*` env exported) and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
 
 ### "The synthesized answer is wrong"
 

src/cli.ts

@@ -365,12 +365,6 @@ 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}`);
@@ -470,7 +464,11 @@ async function main() {
     // routed path. Date → ISO string; bigint → string (postgres.js shape);
     // Buffer → object. Microsecond-cost; eliminates a whole drift bug class.
     const result = JSON.parse(JSON.stringify(rawResult, bigintToStringReplacer));
-    const output = formatResult(op.name, result);
+    // #380 pass-through: `--json` (undeclared on most ops, promised by docs)
+    // emits the raw op result instead of the human formatter.
+    const output = params.json === true
+      ? JSON.stringify(result, null, 2) + '\n'
+      : formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     // v0.42.20.0 (codex D4): on error, set exitCode + return so the `finally`
@@ -553,7 +551,10 @@ async function runThinClientRouted(
       signal: sigintController.signal,
     });
     const result = unpackToolResult(raw);
-    const output = formatResult(op.name, result);
+    // #380: same --json seam as the local-engine path (renderer parity).
+    const output = params.json === true
+      ? JSON.stringify(result, null, 2) + '\n'
+      : formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     if (e instanceof RemoteMcpError) {
@@ -763,14 +764,28 @@ export function resolveQueryImage(
   return { path: imagePath, base64, mime };
 }
 
+/**
+ * #380: undeclared flags that are honored DOWNSTREAM of parseOpArgs and must
+ * keep passing through when unknown flags become hard errors:
+ *   - source     → makeContext's resolveSourceId (the --source axis)
+ *   - brain      → the mount/brain routing axis (docs promise the flag)
+ *   - dry_run    → makeContext's ctx.dryRun (ops without a declared dry_run)
+ *   - json       → raw-JSON output seam (local + thin-client paths)
+ */
+const PASSTHROUGH_VALUE_FLAGS = new Set(['source', 'brain']);
+const PASSTHROUGH_BOOL_FLAGS = new Set(['dry_run', 'json']);
+
 export function parseOpArgs(op: Operation, args: string[]): Record<string, unknown> {
   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>();
+  const cliName = op.cliHints?.name || op.name;
+  const MAX_STDIN = 5_000_000; // 5MB cap, shared by stdin and --file
+  // #380: `--file <path>` fills the op's declared stdin param (put's `content`)
+  // from a file. Driven by cliHints.stdin — no per-op hard-coding — and
+  // disabled when the op declares a real `file` param of its own.
+  const fileParam = op.cliHints?.stdin && !op.params.file ? op.cliHints.stdin : undefined;
+  let filePath: string | undefined;
 
   for (let i = 0; i < args.length; i++) {
     const arg = args[i];
@@ -784,40 +799,79 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
         }
       }
       const key = arg.slice(2).replace(/-/g, '_');
+      if (fileParam && key === 'file') {
+        if (i + 1 >= args.length) {
+          console.error(`Error: ${arg} requires a value.`);
+          process.exit(1);
+        }
+        filePath = args[++i];
+        continue;
+      }
       const paramDef = op.params[key];
-      if (paramDef?.type === 'boolean') {
+      if (!paramDef) {
+        if (PASSTHROUGH_BOOL_FLAGS.has(key)) {
+          params[key] = true;
+          continue;
+        }
+        if (PASSTHROUGH_VALUE_FLAGS.has(key)) {
+          if (i + 1 >= args.length) {
+            console.error(`Error: ${arg} requires a value.`);
+            process.exit(1);
+          }
+          params[key] = args[++i];
+          continue;
+        }
+        // #380: unknown flags were silently swallowed into params, so typos
+        // like `put --file` created empty pages instead of erroring.
+        console.error(`Unknown option for gbrain ${cliName}: ${arg}`);
+        console.error(`Run 'gbrain ${cliName} --help' for valid flags.`);
+        process.exit(1);
+      }
+      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]);
+        if (paramDef.type === 'number') params[key] = Number(params[key]);
+      } else {
+        console.error(`Error: ${arg} requires a value.`);
+        process.exit(1);
       }
     } else if (posIdx < positional.length) {
       const key = positional[posIdx++];
       const paramDef = op.params[key];
-      if (params[key] !== undefined && params[key] !== (paramDef?.type === 'number' ? Number(arg) : arg)) {
-        console.error(`Warning: positional <${key}> overrides the earlier --${key.replace(/_/g, '-')} value ${JSON.stringify(params[key])}.`);
-      }
       params[key] = paramDef?.type === 'number' ? Number(arg) : arg;
-      positionallySet.add(key);
     }
   }
 
+  // #380: resolve --file AFTER the loop so --file/--content conflicts are
+  // caught in either order.
+  if (filePath !== undefined && fileParam) {
+    if (params[fileParam] !== undefined) {
+      console.error(`Error: use only one of --file, --${fileParam}, or stdin for gbrain ${cliName}.`);
+      process.exit(1);
+    }
+    let fileContent: string;
+    try {
+      fileContent = readFileSync(filePath, 'utf-8');
+    } catch (e) {
+      console.error(`Error: cannot read --file ${filePath}: ${e instanceof Error ? e.message : String(e)}`);
+      process.exit(1);
+    }
+    if (Buffer.byteLength(fileContent, 'utf-8') > MAX_STDIN) {
+      console.error(`Error: file content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
+      process.exit(1);
+    }
+    params[fileParam] = fileContent;
+  }
+
   // Read stdin for content params
   if (op.cliHints?.stdin && !params[op.cliHints.stdin] && !process.stdin.isTTY) {
     const stdinContent = readFileSync(0, 'utf-8');
-    const MAX_STDIN = 5_000_000; // 5MB
     if (Buffer.byteLength(stdinContent, 'utf-8') > MAX_STDIN) {
       console.error(`Error: stdin content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
     }
-    // #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;
+    params[op.cliHints.stdin] = stdinContent;
   }
 
   return params;
@@ -2274,6 +2328,10 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${key}>` : `  --${key.replace(/_/g, '-')}`;
       console.log(`${prefix.padEnd(28)} ${def.description || ''}${req}`);
     }
+    // #380: ops that read stdin also accept --file <path> (parseOpArgs).
+    if (op.cliHints?.stdin && !op.params.file) {
+      console.log(`${'  --file <path>'.padEnd(28)} Read ${op.cliHints.stdin} from a file (alternative to --${op.cliHints.stdin} or stdin)`);
+    }
   }
 }
 

src/commands/lint.ts

@@ -48,7 +48,6 @@ 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/import-file.ts

@@ -301,17 +301,6 @@ 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.
@@ -325,17 +314,7 @@ export async function importFromContent(
     };
   }
 
-  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})`);
-  }
+  const parsed = parseMarkdown(content, slug + '.md', { activePack: opts.activePack });
 
   // v0.42 (#1699 trust boundary): strip gate-owned markers from UNTRUSTED
   // input. parseMarkdown preserves every frontmatter key except type/title/

src/core/markdown.ts

@@ -11,8 +11,7 @@ export type ParseValidationCode =
   | 'NULL_BYTES'
   | 'NESTED_QUOTES'
   | 'NON_STRING_FIELD'
-  | 'EMPTY_FRONTMATTER'
-  | 'MULTI_FRONTMATTER';
+  | 'EMPTY_FRONTMATTER';
 
 export interface ParseValidationError {
   code: ParseValidationCode;
@@ -332,50 +331,6 @@ 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

@@ -769,7 +769,7 @@ const get_page: Operation = {
 
 const put_page: Operation = {
   name: 'put_page',
-  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. For large content on Windows (pipe-buffer limit ~45KB) or any file-as-input workflow, use `gbrain capture --file PATH --slug SLUG` — capture reads the file as a Buffer with a binary-NUL guard and adds provenance write-through (v0.39.3.0).',
+  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. On the CLI, `gbrain put SLUG --file PATH` reads content from a file (also `--content` or stdin). For provenance write-through and a binary-NUL guard, prefer `gbrain capture --file PATH --slug SLUG` (v0.39.3.0).',
   params: {
     slug: { type: 'string', required: true, description: 'Page slug' },
     content: { type: 'string', required: true, description: 'Full markdown content with YAML frontmatter' },
@@ -1384,7 +1384,10 @@ const list_pages: Operation = {
   params: {
     type: { type: 'string', description: 'Filter by page type' },
     tag: { type: 'string', description: 'Filter by tag' },
-    limit: { type: 'number', description: 'Max results (default 50)' },
+    limit: { type: 'number', description: 'Max results (default 50, capped at 100 — use offset to paginate beyond)' },
+    // #2876: the 100-row cap was silent and there was no way past it even
+    // though both engines already support OFFSET on listPages.
+    offset: { type: 'number', description: 'Skip first N results (pagination; pair with limit)' },
     // v0.29 — surface filter that already exists on PageFilters.
     updated_after: {
       type: 'string',
@@ -1415,6 +1418,10 @@ const list_pages: Operation = {
       type: p.type as any,
       tag: p.tag as string,
       limit: clampSearchLimit(p.limit as number | undefined, 50, 100),
+      // #2876: thread pagination through (engines already honor offset).
+      offset: Number.isFinite(p.offset as number) && (p.offset as number) > 0
+        ? Math.floor(p.offset as number)
+        : undefined,
       includeDeleted: (p.include_deleted as boolean) === true,
       updated_after: typeof p.updated_after === 'string' ? p.updated_after : undefined,
       sort,

test/cli-args.test.ts

@@ -1,12 +1,41 @@
-import { afterEach, describe, expect, test } from 'bun:test';
-import { spawnSync } from 'child_process';
-import { join, resolve } from 'path';
-import { mkdtempSync, rmSync } from 'fs';
+import { describe, expect, test } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync } from 'fs';
 import { tmpdir } from 'os';
+import { join } from 'path';
 import { parseOpArgs } from '../src/cli.ts';
 import { operationsByName } from '../src/core/operations.ts';
 
 describe('parseOpArgs', () => {
+  // #380: `gbrain put SLUG --file PATH` reads content from the file instead
+  // of silently swallowing the flag and creating an empty page.
+  test('put --file reads the stdin param (content) from a file', () => {
+    const dir = mkdtempSync(join(tmpdir(), 'gbrain-put-file-'));
+    try {
+      const pagePath = join(dir, 'page.md');
+      writeFileSync(pagePath, '# From file\n\nBody loaded from --file.\n');
+      const params = parseOpArgs(operationsByName.put_page, ['concepts/from-file', '--file', pagePath]);
+      expect(params.slug).toBe('concepts/from-file');
+      expect(params.content).toBe('# From file\n\nBody loaded from --file.\n');
+    } finally {
+      rmSync(dir, { recursive: true, force: true });
+    }
+  });
+
+  // #380 regression guard: undeclared-but-honored flags must keep passing
+  // through when unknown flags become hard errors (--source is read by
+  // makeContext; --json by the output seam; --dry-run by ctx.dryRun).
+  test('pass-through allowlist flags survive on ops that do not declare them', () => {
+    const params = parseOpArgs(operationsByName.get_page, [
+      'people/alice-example', '--source', 'wiki', '--json', '--dry-run',
+    ]);
+    expect(params).toEqual({
+      slug: 'people/alice-example',
+      source: 'wiki',
+      json: true,
+      dry_run: true,
+    });
+  });
+
   test('--no-<boolean> maps to false without consuming the next flag', () => {
     const params = parseOpArgs(operationsByName.query, [
       'freshEmbedSourceScope code source',
@@ -24,70 +53,5 @@ 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.test.ts

@@ -1,5 +1,5 @@
 import { describe, test, expect } from 'bun:test';
-import { existsSync, mkdtempSync, readFileSync, rmSync } from 'fs';
+import { existsSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 
@@ -120,6 +120,76 @@ describe('CLI dispatch integration', () => {
     expect(exitCode).toBe(0);
   });
 
+  // #380 / PR #856: put --help documents the --file input path.
+  test('put --help documents --file input', async () => {
+    const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'put', '--help'], {
+      cwd: repoRoot,
+      stdout: 'pipe',
+      stderr: 'pipe',
+    });
+    const stdout = await new Response(proc.stdout).text();
+    const exitCode = await proc.exited;
+    expect(stdout).toContain('Usage: gbrain put');
+    expect(stdout).toContain('--file <path>');
+    expect(exitCode).toBe(0);
+  });
+
+  // #380: unknown flags on shared ops are a hard error (previously silently
+  // swallowed into params — `put --file` created empty pages). parseOpArgs
+  // runs BEFORE engine connect, so the error must fire without a brain.
+  test('unknown shared-op flags fail before DB connection', async () => {
+    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-unknown-flag-'));
+    try {
+      const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'get', 'people/alice', '--bogus'], {
+        cwd: repoRoot,
+        stdout: 'pipe',
+        stderr: 'pipe',
+        env: isolatedEnv(home),
+      });
+      const stderr = await new Response(proc.stderr).text();
+      const exitCode = await proc.exited;
+      expect(stderr).toContain('Unknown option for gbrain get: --bogus');
+      expect(stderr).not.toContain('No brain configured');
+      expect(exitCode).toBe(1);
+    } finally {
+      rmSync(home, { recursive: true, force: true });
+    }
+  });
+
+  test('put rejects combining --file and --content', async () => {
+    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-conflict-'));
+    try {
+      const pagePath = join(home, 'page.md');
+      writeFileSync(pagePath, 'file body\n');
+      const proc = Bun.spawn(
+        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--content', 'inline', '--file', pagePath],
+        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
+      );
+      const stderr = await new Response(proc.stderr).text();
+      const exitCode = await proc.exited;
+      expect(stderr).toContain('use only one of --file, --content, or stdin');
+      expect(exitCode).toBe(1);
+    } finally {
+      rmSync(home, { recursive: true, force: true });
+    }
+  });
+
+  test('put --file with a missing path errors instead of writing an empty page', async () => {
+    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-missing-file-'));
+    try {
+      const proc = Bun.spawn(
+        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--file', join(home, 'nope.md')],
+        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
+      );
+      const stderr = await new Response(proc.stderr).text();
+      const exitCode = await proc.exited;
+      expect(stderr).toContain('cannot read --file');
+      expect(exitCode).toBe(1);
+    } finally {
+      rmSync(home, { recursive: true, force: true });
+    }
+  });
+
   test('upgrade --help prints usage without running upgrade', async () => {
     const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'upgrade', '--help'], {
       cwd: repoRoot,

test/import-file.test.ts

@@ -708,32 +708,3 @@ 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/list-pages-offset.test.ts

@@ -0,0 +1,55 @@
+import { describe, test, expect } from 'bun:test';
+import { operationsByName } from '../src/core/operations.ts';
+
+/**
+ * #2876: `gbrain list --limit` silently clamped at 100 with no pagination.
+ * list_pages now declares `offset` (both engines already supported it on
+ * PageFilters) and the limit description discloses the 100-row cap.
+ */
+describe('list_pages pagination (#2876)', () => {
+  const listPagesOp = operationsByName.list_pages;
+
+  function makeCtx(captured: unknown[]) {
+    return {
+      engine: {
+        listPages: async (filters: unknown) => {
+          captured.push(filters);
+          return [];
+        },
+      },
+      config: { engine: 'pglite' },
+      logger: { info() {}, warn() {}, error() {} },
+      dryRun: false,
+      remote: false,
+      sourceId: 'default',
+    } as any;
+  }
+
+  test('declares offset param and discloses the 100-row cap on limit', () => {
+    expect(listPagesOp.params.offset).toBeDefined();
+    expect(listPagesOp.params.offset.type).toBe('number');
+    expect(listPagesOp.params.limit.description).toContain('100');
+  });
+
+  test('threads offset through to engine.listPages', async () => {
+    const captured: any[] = [];
+    await listPagesOp.handler(makeCtx(captured), { limit: 10, offset: 30 });
+    expect(captured[0].offset).toBe(30);
+    expect(captured[0].limit).toBe(10);
+  });
+
+  test('drops negative, non-finite, and zero offsets', async () => {
+    const captured: any[] = [];
+    const ctx = makeCtx(captured);
+    await listPagesOp.handler(ctx, { offset: -5 });
+    await listPagesOp.handler(ctx, { offset: Infinity });
+    await listPagesOp.handler(ctx, { offset: 0 });
+    for (const f of captured) expect(f.offset).toBeUndefined();
+  });
+
+  test('floors fractional offsets', async () => {
+    const captured: any[] = [];
+    await listPagesOp.handler(makeCtx(captured), { offset: 7.9 });
+    expect(captured[0].offset).toBe(7);
+  });
+});

test/markdown-validation.test.ts

@@ -256,56 +256,6 @@ 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 });