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

@@ -464,7 +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`
@@ -547,7 +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) {
@@ -757,10 +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;
+  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];
@@ -774,12 +799,42 @@ 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) {
         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++];
@@ -788,10 +843,30 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
     }
   }
 
+  // #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 ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
@@ -2253,6 +2328,10 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${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/core/ai/anthropic-key.ts

@@ -18,22 +18,12 @@
 import { loadConfig } from '../config.ts';
 
 export function hasAnthropicKey(): boolean {
-  return resolveAnthropicKey() !== undefined;
-}
-
-/**
- * Resolve the actual key value: env first, then the gbrain config file.
- * Callers constructing an Anthropic client directly (e.g. the legacy
- * subagent path) must pass this as `apiKey` — a bare `new Anthropic()`
- * only sees env, so launchd/MCP workers with config-stored keys fail.
- */
-export function resolveAnthropicKey(): string | undefined {
-  if (process.env.ANTHROPIC_API_KEY) return process.env.ANTHROPIC_API_KEY;
+  if (process.env.ANTHROPIC_API_KEY) return true;
   try {
     const cfg = loadConfig();
-    if (cfg?.anthropic_api_key) return cfg.anthropic_api_key;
+    if (cfg?.anthropic_api_key) return true;
   } catch {
     // loadConfig may throw on first-run installs; treat as no key available.
   }
-  return undefined;
+  return false;
 }

src/core/minions/handlers/subagent.ts

@@ -48,7 +48,6 @@ import {
   logSubagentHeartbeat,
 } from './subagent-audit.ts';
 import { resolveModel, isAnthropicProvider, TIER_DEFAULTS } from '../../model-config.ts';
-import { resolveAnthropicKey } from '../../ai/anthropic-key.ts';
 import { buildSystemPrompt, DEFAULT_SUBAGENT_SYSTEM } from '../system-prompt.ts';
 import { toolLoop as gatewayToolLoop } from '../../ai/gateway.ts';
 import type { ChatToolDef, ChatMessage, ChatBlock, ChatResult, ToolHandler } from '../../ai/gateway.ts';
@@ -187,10 +186,7 @@ export function makeSubagentHandler(deps: SubagentDeps) {
   // lives at sdk.messages.create. Assigning sdk.messages directly gets the
   // right object; JS method-call semantics preserve `this` at the call
   // site (subagent.ts invokes client.create(...) with client === sdk.messages).
-  // Resolve the key env-first, then config (anthropic_api_key) — a bare
-  // new Anthropic() only reads env, so launchd/MCP workers whose key lives
-  // in the gbrain config file would fail auth (#2048).
-  const makeAnthropic = deps.makeAnthropic ?? (() => new Anthropic({ apiKey: resolveAnthropicKey() }));
+  const makeAnthropic = deps.makeAnthropic ?? (() => new Anthropic());
   const client: MessagesClient = deps.client ?? makeAnthropic().messages;
   const config = deps.config ?? loadConfig() ?? ({ engine: 'postgres' } as GBrainConfig);
   const rateLeaseKey = deps.rateLeaseKey ?? DEFAULT_RATE_KEY;

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,
@@ -4562,8 +4569,7 @@ const list_schema_packs: Operation = {
     const { existsSync, readdirSync } = await import('node:fs');
     const { join } = await import('node:path');
     const { gbrainPath } = await import('./config.ts');
-    const { BUNDLED_PACK_NAMES } = await import('./schema-pack/bundled.ts');
-    const bundled = [...BUNDLED_PACK_NAMES];
+    const bundled = ['gbrain-base', 'gbrain-recommended'];
     const installedDir = gbrainPath('schema-packs');
     const installed: string[] = [];
     if (existsSync(installedDir)) {

src/core/schema-pack/bundled.ts

@@ -1,24 +0,0 @@
-// Bundled schema-pack registry — single source of truth for the packs that
-// ship in src/core/schema-pack/base/. Keep every bundled-pack consumer
-// (CLI/MCP inspection, active-pack loading, mutation guards, upgrade
-// discovery) on this one list so they cannot drift.
-//
-// v0.39 T8 — gbrain-base + gbrain-recommended.
-// v0.41 T4 — lens packs: creator, investor, engineer, everything (meta-pack).
-// v0.42 type-unification — gbrain-base-v2, the 15-type canonical successor.
-
-export const BUNDLED_PACK_NAMES = [
-  'gbrain-base',
-  'gbrain-recommended',
-  'gbrain-creator',
-  'gbrain-investor',
-  'gbrain-engineer',
-  'gbrain-everything',
-  'gbrain-base-v2',
-] as const;
-
-export type BundledPackName = typeof BUNDLED_PACK_NAMES[number];
-
-export function isBundledPackName(name: string): name is BundledPackName {
-  return (BUNDLED_PACK_NAMES as readonly string[]).includes(name);
-}

src/core/schema-pack/load-active.ts

@@ -37,7 +37,6 @@ import {
   type ResolutionInput,
   type ResolutionResult,
 } from './registry.ts';
-import { isBundledPackName } from './bundled.ts';
 
 /**
  * Inputs the caller (operations.ts handler / engine query path) provides.
@@ -93,7 +92,28 @@ export function _resetPackLocatorForTests(): void {
  * throwing UnknownPackError with a paste-ready install hint.
  */
 function defaultPackLocator(name: string): string | null {
-  if (isBundledPackName(name)) {
+  // v0.39 T8 — bundled packs registry. gbrain-base + gbrain-recommended
+  // ship in src/core/schema-pack/base/. Add a new entry here to bundle
+  // additional canonical packs.
+  //
+  // v0.41 T4 — lens packs join the bundle: creator (atoms + concepts +
+  // extract_atoms/synthesize_concepts phases), investor (theses + bet
+  // resolution + 3 calibration domains), engineer (gstack-learnings bridge
+  // + 3 calibration domains), everything (meta-pack stacking all three
+  // via extends + borrow_from). Each ships as a real YAML at base/<name>.yaml.
+  const BUNDLED: ReadonlyArray<string> = [
+    'gbrain-base',
+    'gbrain-recommended',
+    'gbrain-creator',
+    'gbrain-investor',
+    'gbrain-engineer',
+    'gbrain-everything',
+    // v0.42 type-unification: 15-type canonical successor to gbrain-base.
+    // Ships as install default (Lane E T17) + via gbrain onboard pack
+    // upgrade flow (the unify-types Minion handler).
+    'gbrain-base-v2',
+  ];
+  if (BUNDLED.includes(name)) {
     // Resolve bundled YAML relative to this source file. Works in both
     // direct-bun execution and bun --compile binaries.
     const here = dirname(fileURLToPath(import.meta.url));

src/core/schema-pack/loader.ts

@@ -159,29 +159,6 @@ export function parseYamlMini(content: string): unknown {
     return parseMapping(baseIndent);
   }
 
-  function parseBlockScalar(parentIndent: number, folded: boolean): string {
-    const contentIndent = parentIndent + 2;
-    const out: string[] = [];
-    while (i < lines.length) {
-      const raw = lines[i];
-      // Inside a block scalar everything is literal content — '#' is NOT a
-      // comment here, so use the raw line (no stripComment / isBlank).
-      if (raw.trim() === '') {
-        out.push('');
-        i++;
-        continue;
-      }
-      const indent = indentOf(raw);
-      if (indent <= parentIndent) break;
-      out.push(raw.slice(Math.min(contentIndent, indent)));
-      i++;
-    }
-    if (folded) {
-      return out.join(' ').replace(/\s+$/u, '');
-    }
-    return out.join('\n').replace(/\n+$/u, '');
-  }
-
   function parseSequence(baseIndent: number): unknown[] {
     const result: unknown[] = [];
     while (i < lines.length) {
@@ -250,10 +227,6 @@ export function parseYamlMini(content: string): unknown {
           i++;
           if (rest2 === '') {
             map[key2] = parseBlock(nextIndent + 2);
-          } else if (rest2 === '|' || rest2 === '|-' || rest2 === '|+') {
-            map[key2] = parseBlockScalar(nextIndent, false);
-          } else if (rest2 === '>' || rest2 === '>-' || rest2 === '>+') {
-            map[key2] = parseBlockScalar(nextIndent, true);
           } else {
             map[key2] = parseScalar(rest2);
           }
@@ -284,10 +257,6 @@ export function parseYamlMini(content: string): unknown {
       i++;
       if (rest === '') {
         result[key] = parseBlock(indent + 2);
-      } else if (rest === '|' || rest === '|-' || rest === '|+') {
-        result[key] = parseBlockScalar(indent, false);
-      } else if (rest === '>' || rest === '>-' || rest === '>+') {
-        result[key] = parseBlockScalar(indent, true);
       } else {
         result[key] = parseScalar(rest);
       }

src/core/schema-pack/mutate.ts

@@ -65,7 +65,6 @@ import { invalidateQueryCache } from './query-cache-invalidator.ts';
 import { logMutationFailure, logMutationSuccess, type MutationActor, type MutationOp } from './mutate-audit.ts';
 import { runFilePlaneLintRules } from './lint-rules.ts';
 import { withPackLock, type PackLockOpts } from './pack-lock.ts';
-import { BUNDLED_PACK_NAMES as BUNDLED_PACK_NAME_LIST } from './bundled.ts';
 import type { BrainEngine } from '../engine.ts';
 
 export type PackFileFormat = 'json' | 'yaml';
@@ -94,7 +93,7 @@ export class SchemaPackMutationError extends Error {
   }
 }
 
-export const BUNDLED_PACK_NAMES = new Set<string>(BUNDLED_PACK_NAME_LIST);
+export const BUNDLED_PACK_NAMES = new Set(['gbrain-base', 'gbrain-recommended', 'gbrain-base-v2']);
 
 export interface MutateResult {
   /** Pack name that was mutated. */

test/ai/anthropic-key.test.ts

@@ -10,7 +10,7 @@ import { mkdtempSync, mkdirSync, writeFileSync, rmSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { withEnv } from '../helpers/with-env.ts';
-import { hasAnthropicKey, resolveAnthropicKey } from '../../src/core/ai/anthropic-key.ts';
+import { hasAnthropicKey } from '../../src/core/ai/anthropic-key.ts';
 
 const tmpDirs: string[] = [];
 function freshHome(withConfig?: Record<string, unknown>): string {
@@ -62,35 +62,3 @@ describe('hasAnthropicKey', () => {
     );
   });
 });
-
-describe('resolveAnthropicKey (#2048 — subagent config-key auth)', () => {
-  test('env wins over config', async () => {
-    const home = freshHome({ anthropic_api_key: 'sk-from-config' });
-    await withEnv(
-      { ANTHROPIC_API_KEY: 'sk-from-env', GBRAIN_HOME: home, DATABASE_URL: undefined, GBRAIN_DATABASE_URL: undefined },
-      async () => {
-        expect(resolveAnthropicKey()).toBe('sk-from-env');
-      },
-    );
-  });
-
-  test('config key returned when env unset', async () => {
-    const home = freshHome({ anthropic_api_key: 'sk-from-config' });
-    await withEnv(
-      { ANTHROPIC_API_KEY: undefined, GBRAIN_HOME: home, DATABASE_URL: undefined, GBRAIN_DATABASE_URL: undefined },
-      async () => {
-        expect(resolveAnthropicKey()).toBe('sk-from-config');
-      },
-    );
-  });
-
-  test('neither → undefined', async () => {
-    const home = freshHome();
-    await withEnv(
-      { ANTHROPIC_API_KEY: undefined, GBRAIN_HOME: home, DATABASE_URL: undefined, GBRAIN_DATABASE_URL: undefined },
-      async () => {
-        expect(resolveAnthropicKey()).toBeUndefined();
-      },
-    );
-  });
-});

test/cli-args.test.ts

@@ -1,8 +1,41 @@
 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',

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/lens-pack-manifests.test.ts

@@ -55,13 +55,13 @@ describe('v0.41 T4: all 4 bundled lens packs parse cleanly', () => {
 });
 
 describe('v0.41 T4: bundled registry includes lens packs', () => {
-  test('BUNDLED_PACK_NAMES includes the 4 lens pack names', async () => {
-    // The bundled list moved from load-active.ts to bundled.ts (the
-    // single source of truth); assert the array directly instead of
-    // grepping source text.
-    const { BUNDLED_PACK_NAMES } = await import('../src/core/schema-pack/bundled.ts');
+  test('load-active.ts BUNDLED array source includes the 4 lens pack names', () => {
+    const loadActiveSrc = readFileSync(
+      join(here, '..', 'src', 'core', 'schema-pack', 'load-active.ts'),
+      'utf-8',
+    );
     for (const name of PACK_NAMES) {
-      expect(BUNDLED_PACK_NAMES).toContain(name);
+      expect(loadActiveSrc).toContain(`'${name}'`);
     }
   });
 });

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/operations-schema-pack.test.ts

@@ -149,9 +149,6 @@ describe('list_schema_packs', () => {
       seedPack('mine');
       const result = await operationsByName.list_schema_packs!.handler(ctxOf(), {}) as { bundled: string[]; installed: string[] };
       expect(result.bundled).toContain('gbrain-base');
-      expect(result.bundled).toContain('gbrain-recommended');
-      expect(result.bundled).toContain('gbrain-base-v2');
-      expect(result.bundled).toContain('gbrain-investor');
       expect(result.installed).toContain('mine');
     });
   });

test/schema-cli.test.ts

@@ -64,14 +64,11 @@ describe('gbrain schema CLI (Phase C)', () => {
     expect(r.stdout + r.stderr).toMatch(/schema|active|list|show|validate|use/i);
   });
 
-  test('schema list shows all bundled packs', () => {
+  test('schema list shows gbrain-base bundled', () => {
     const r = gbrain(['schema', 'list']);
     expect(r.code).toBe(0);
     expect(r.stdout).toContain('Bundled packs:');
     expect(r.stdout).toContain('gbrain-base');
-    expect(r.stdout).toContain('gbrain-recommended');
-    expect(r.stdout).toContain('gbrain-base-v2');
-    expect(r.stdout).toContain('gbrain-investor');
   });
 
   test('schema show gbrain-base prints manifest details', () => {
@@ -100,40 +97,6 @@ describe('gbrain schema CLI (Phase C)', () => {
     expect(r.stdout).toContain('valid manifest');
   });
 
-  test('schema show/validate exposes bundled gbrain-recommended', () => {
-    const show = gbrain(['schema', 'show', 'gbrain-recommended']);
-    expect(show.code).toBe(0);
-    expect(show.stdout).toContain('gbrain-recommended v1.0.0');
-    expect(show.stdout).toContain('Page types (');
-    expect(show.stdout).toContain('meeting :: temporal');
-
-    const validate = gbrain(['schema', 'validate', 'gbrain-recommended']);
-    expect(validate.code).toBe(0);
-    expect(validate.stdout).toContain('valid manifest');
-  });
-
-  test('schema show exposes bundled gbrain-base-v2 successor pack', () => {
-    const r = gbrain(['schema', 'show', 'gbrain-base-v2']);
-    expect(r.code).toBe(0);
-    expect(r.stdout).toContain('gbrain-base-v2 v1.0.0');
-    expect(r.stdout).toContain('Page types (');
-    expect(r.stdout).toContain('Link verbs (14)');
-  });
-
-  test('schema active loads configured gbrain-recommended with real types', () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-schema-active-recommended-'));
-    try {
-      mkdirSync(join(home, '.gbrain'), { recursive: true });
-      writeFileSync(join(home, '.gbrain', 'config.json'), JSON.stringify({ schema_pack: 'gbrain-recommended' }), 'utf-8');
-      const r = gbrain(['schema', 'active'], { GBRAIN_HOME: home });
-      expect(r.code).toBe(0);
-      expect(r.stdout).toContain('Active pack: gbrain-recommended');
-      expect(r.stdout).not.toContain('Page types: 0');
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
   test('schema active reports default resolution', () => {
     const r = gbrain(['schema', 'active']);
     expect(r.code).toBe(0);

test/schema-pack-loader.test.ts

@@ -345,34 +345,6 @@ describe('YAML mini-parser', () => {
     expect(result.types[1].weight).toBe(2);
   });
 
-  test('parses block scalar without swallowing following keys', () => {
-    const yaml = `name: blocky
-description: |
-  First line.
-  Second line.
-page_types:
-  - name: meeting
-    primitive: temporal
-    path_prefixes:
-      - meetings/
-    aliases: []
-    extractable: true
-    expert_routing: false`;
-    const result = parseYamlMini(yaml) as { description: string; page_types: Array<Record<string, unknown>> };
-    expect(result.description).toBe('First line.\nSecond line.');
-    expect(result.page_types).toHaveLength(1);
-    expect(result.page_types[0].name).toBe('meeting');
-  });
-
-  test('block scalar keeps # as literal content, not a comment', () => {
-    const yaml = `description: |
-  See issue #2029 for context.
-name: hashy`;
-    const result = parseYamlMini(yaml) as Record<string, unknown>;
-    expect(result.description).toBe('See issue #2029 for context.');
-    expect(result.name).toBe('hashy');
-  });
-
   test('strips comments', () => {
     const result = parseYamlMini('# top comment\nname: value # inline comment') as Record<string, unknown>;
     expect(result.name).toBe('value');
@@ -402,27 +374,6 @@ extends: null`;
     const pack = loadPackFromString(json, 'fixture.json');
     expect(pack.name).toBe('json-pack');
   });
-
-  test('loads block-scalar pack descriptions without losing page types', () => {
-    const pack = loadPackFromString(`api_version: gbrain-schema-pack-v1
-name: recommended-fixture
-version: 1.0.0
-extends: gbrain-base
-description: |
-  Operational starter pack.
-page_types:
-  - name: meeting
-    primitive: temporal
-    path_prefixes:
-      - meetings/
-    aliases: []
-    extractable: true
-    expert_routing: false
-link_types: []`, 'fixture.yaml');
-    expect(pack.name).toBe('recommended-fixture');
-    expect(pack.extends).toBe('gbrain-base');
-    expect(pack.page_types.map((t) => t.name)).toContain('meeting');
-  });
 });
 
 describe('ReDoS guard', () => {

test/schema-pack-mutate.test.ts

@@ -103,10 +103,7 @@ describe('locateMutablePackFile — bundled guard', () => {
     expect(BUNDLED_PACK_NAMES.has('gbrain-recommended')).toBe(true);
     // v0.42 (T22): gbrain-base-v2 joins the bundled set.
     expect(BUNDLED_PACK_NAMES.has('gbrain-base-v2')).toBe(true);
-    // Derived from the single bundled registry — the lens packs (creator,
-    // investor, engineer, everything) are read-only too.
-    expect(BUNDLED_PACK_NAMES.has('gbrain-investor')).toBe(true);
-    expect(BUNDLED_PACK_NAMES.size).toBe(7);
+    expect(BUNDLED_PACK_NAMES.size).toBe(3);
   });
 
   it('rejects gbrain-base-v2 with PACK_READONLY (bundled guard)', () => {