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"
 

skills/article-enrichment/SKILL.md

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

skills/book-mirror/SKILL.md

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

skills/conventions/reference-entities.md

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

skills/enrich/SKILL.md

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

skills/maintain/SKILL.md

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

src/cli.ts

@@ -54,7 +54,7 @@ export function bigintToStringReplacer(_key: string, value: unknown): unknown {
 }
 
 // CLI-only commands that bypass the operation layer
-export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'reference', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
+export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
 // CLI-only commands whose handlers print their own --help text. These are
 // excluded from the generic short-circuit so detailed per-command and
 // per-subcommand usage stays reachable.
@@ -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 ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
@@ -1652,11 +1727,6 @@ async function handleCliOnly(command: string, args: string[]) {
         await runFiles(engine, args);
         break;
       }
-      case 'reference': {
-        const { runReference } = await import('./commands/reference.ts');
-        await runReference(engine, args);
-        break;
-      }
       case 'embed': {
         const { runEmbed } = await import('./commands/embed.ts');
         await runEmbed(engine, args);
@@ -2258,6 +2328,10 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${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/reference.ts

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

src/core/onboard/checks.ts

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

src/core/onboard/init-nudge.ts

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

src/core/operations.ts

@@ -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,

src/core/pglite-engine.ts

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

src/core/postgres-engine.ts

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

src/core/reference-flag.ts

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

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/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/reference-flag.test.ts

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