fix(dream): keep dream --dry-run --json stdout clean of embed summaries (#394)

The cycle's embed phase called runEmbedCore with no output suppression, so
the '[dry-run] Would embed ...' / 'Embedded N chunks ...' slog summaries
landed on stdout ahead of the JSON CycleReport, breaking the documented
stdout-clean-for-JSON contract (docs/progress-events.md).

Adds EmbedOpts.quiet gating the human stdout summary slog sites in
embed.ts (embedPage, embedAll, embedAllStale); the cycle's runPhaseEmbed
sets quiet: true since it reports counts via its own PhaseResult. Errors
and warnings still go to stderr regardless.

Takeover of #854 (same approach, reimplemented on current master — the
original patch predates the slog migration and the widened
embedAll/embedAllStale signatures). Regression test ported from #854.

Co-authored-by: Kage18 <Kage18@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/tutorials/company-brain.md

@@ -223,16 +223,14 @@ 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"
+gbrain search "performance review" --remote
 ```
 
-(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"
+gbrain search "performance review" --remote
 ```
 
 Bob should see the performance-review notes from `internal`, plus anything related from `shared`. He shouldn't see anything that lives only in `customers`.
@@ -516,7 +514,7 @@ 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> --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.
+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.
 
 ### "The synthesized answer is wrong"
 

src/cli.ts

@@ -464,11 +464,7 @@ 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));
-    // #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);
+    const output = 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`
@@ -551,10 +547,7 @@ async function runThinClientRouted(
       signal: sigintController.signal,
     });
     const result = unpackToolResult(raw);
-    // #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);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     if (e instanceof RemoteMcpError) {
@@ -764,28 +757,10 @@ 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];
@@ -799,42 +774,12 @@ 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) {
-        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') {
+      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]);
-      } else {
-        console.error(`Error: ${arg} requires a value.`);
-        process.exit(1);
+        if (paramDef?.type === 'number') params[key] = Number(params[key]);
       }
     } else if (posIdx < positional.length) {
       const key = positional[posIdx++];
@@ -843,30 +788,10 @@ 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 ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
@@ -2328,10 +2253,6 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${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/embed.ts

@@ -107,6 +107,14 @@ export interface EmbedOpts {
    * runs lock every source in sorted order. dryRun skips it.
    */
   singleFlight?: boolean;
+  /**
+   * #394: suppress human stdout summaries (the `[dry-run] Would embed ...` /
+   * `Embedded N chunks ...` slog lines). Set by structured-output callers —
+   * the cycle's embed phase (dream --json must keep stdout JSON-clean per
+   * docs/progress-events.md) reports counts via its own PhaseResult instead.
+   * Errors/warnings still go to stderr regardless.
+   */
+  quiet?: boolean;
 }
 
 /**
@@ -253,7 +261,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
     for (const s of opts.slugs) {
       if (isAborted(opts.signal)) break; // #1737: stop the per-slug loop on abort
       try {
-        await embedPage(engine, s, !!opts.dryRun, result, opts.sourceId, opts.signal);
+        await embedPage(engine, s, !!opts.dryRun, result, opts.sourceId, opts.signal, opts.quiet);
       } catch (e: unknown) {
         serr(`  Error embedding ${s}: ${e instanceof Error ? e.message : e}`);
       }
@@ -347,6 +355,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
         catchUp: opts.catchUp,
         pacer,
         paceMaxConcurrency,
+        quiet: opts.quiet,
       }, opts.signal);
     } finally {
       // E1: surface pacing telemetry (human + structured) when pacing was on.
@@ -376,7 +385,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
     return result;
   }
   if (opts.slug) {
-    await embedPage(engine, opts.slug, !!opts.dryRun, result, opts.sourceId, opts.signal);
+    await embedPage(engine, opts.slug, !!opts.dryRun, result, opts.sourceId, opts.signal, opts.quiet);
     return result;
   }
   throw new Error('No embed target specified. Pass { slug }, { slugs }, { all }, or { stale }.');
@@ -521,6 +530,7 @@ async function embedPage(
   result: EmbedResult,
   sourceId?: string,
   signal?: AbortSignal,
+  quiet?: boolean,
 ) {
   const opts = sourceId ? { sourceId } : undefined;
   const page = await engine.getPage(slug, opts);
@@ -565,7 +575,7 @@ async function embedPage(
   result.skipped += chunks.length - toEmbed.length;
 
   if (toEmbed.length === 0) {
-    slog(`${slug}: all ${chunks.length} chunks already embedded`);
+    if (!quiet) slog(`${slug}: all ${chunks.length} chunks already embedded`);
     result.pages_processed++;
     return;
   }
@@ -602,7 +612,7 @@ async function embedPage(
   }
   result.embedded += toEmbed.length;
   result.pages_processed++;
-  slog(`${slug}: embedded ${toEmbed.length} chunks`);
+  if (!quiet) slog(`${slug}: embedded ${toEmbed.length} chunks`);
 }
 
 async function embedAll(
@@ -620,6 +630,8 @@ async function embedAll(
     pacer?: DbPacer;
     /** Resolved concurrency cap (E-1: the worker count, no separate permit). */
     paceMaxConcurrency?: number;
+    /** #394: suppress human stdout summaries (structured-output callers). */
+    quiet?: boolean;
   },
   signal?: AbortSignal,
 ) {
@@ -763,10 +775,12 @@ async function embedAll(
   });
 
   // Stdout summary preserved for scripts/tests that grep for counts.
-  if (dryRun) {
-    slog(`[dry-run] Would embed ${result.would_embed} chunks across ${pages.length} pages`);
-  } else {
-    slog(`Embedded ${result.embedded} chunks across ${pages.length} pages`);
+  if (!staleOpts?.quiet) {
+    if (dryRun) {
+      slog(`[dry-run] Would embed ${result.would_embed} chunks across ${pages.length} pages`);
+    } else {
+      slog(`Embedded ${result.embedded} chunks across ${pages.length} pages`);
+    }
   }
 }
 
@@ -802,6 +816,8 @@ async function embedAllStale(
     pacer?: DbPacer;
     /** Resolved concurrency cap (E-1: the worker count, no separate permit). */
     paceMaxConcurrency?: number;
+    /** #394: suppress human stdout summaries (structured-output callers). */
+    quiet?: boolean;
   },
   signature?: string,
   externalSignal?: AbortSignal,
@@ -819,7 +835,7 @@ async function embedAllStale(
       signature,
       ...(sourceId && { sourceId }),
     });
-    if (invalidated > 0) {
+    if (invalidated > 0 && !staleOpts?.quiet) {
       slog(`[embed] invalidated ${invalidated} chunk(s) embedded under a prior model signature`);
     }
   }
@@ -830,10 +846,12 @@ async function embedAllStale(
     dryRun && signature ? { ...sourceOpt, signature } : sourceOpt,
   );
   if (staleCount === 0) {
-    if (dryRun) {
-      slog('[dry-run] Would embed 0 chunks (0 stale found)');
-    } else {
-      slog('Embedded 0 chunks (0 stale found)');
+    if (!staleOpts?.quiet) {
+      if (dryRun) {
+        slog('[dry-run] Would embed 0 chunks (0 stale found)');
+      } else {
+        slog('Embedded 0 chunks (0 stale found)');
+      }
     }
     return;
   }
@@ -842,7 +860,7 @@ async function embedAllStale(
     result.would_embed += staleCount;
     result.total_chunks += staleCount;
     if (onProgress) onProgress(1, 1, 0);
-    slog(`[dry-run] Would embed ${staleCount} stale chunks`);
+    if (!staleOpts?.quiet) slog(`[dry-run] Would embed ${staleCount} stale chunks`);
     return;
   }
 
@@ -1082,7 +1100,7 @@ async function embedAllStale(
     if (budgetTimer) clearTimeout(budgetTimer);
   }
 
-  slog(`Embedded ${result.embedded} chunks across ${totalProcessedPages} pages`);
+  if (!staleOpts?.quiet) slog(`Embedded ${result.embedded} chunks across ${totalProcessedPages} pages`);
 
   // #1946 (OV2a): a catch-up pass that completed without being aborted but left
   // chunks unembedded means those chunks are stuck (a non-transient embed

src/core/cycle.ts

@@ -1214,7 +1214,9 @@ async function runPhaseEmbed(engine: BrainEngine, dryRun: boolean, signal?: Abor
     // 10-15 min one) bails within a batch instead of running to completion
     // after the job was killed — which left gbrain_cycle_locks held and
     // wedged every subsequent autopilot cycle.
-    const result = await runEmbedCore(engine, { stale: true, dryRun, signal });
+    // #394: quiet — the cycle reports embed counts via its own PhaseResult;
+    // raw `[dry-run] Would embed ...` stdout lines would corrupt `dream --json`.
+    const result = await runEmbedCore(engine, { stale: true, dryRun, signal, quiet: true });
     const embeddedCount = dryRun ? result.would_embed : result.embedded;
     return {
       phase: 'embed',

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. 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).',
+  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).',
   params: {
     slug: { type: 'string', required: true, description: 'Page slug' },
     content: { type: 'string', required: true, description: 'Full markdown content with YAML frontmatter' },
@@ -1384,10 +1384,7 @@ 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, 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)' },
+    limit: { type: 'number', description: 'Max results (default 50)' },
     // v0.29 — surface filter that already exists on PageFilters.
     updated_after: {
       type: 'string',
@@ -1418,10 +1415,6 @@ 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

@@ -1,41 +1,8 @@
 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, writeFileSync } from 'fs';
+import { existsSync, mkdtempSync, readFileSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 
@@ -120,76 +120,6 @@ 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/dream.test.ts

@@ -292,6 +292,33 @@ describe('runDream — output format', () => {
     expect(parsed).toHaveProperty('totals');
   });
 
+  // #394 / takeover of #854: the embed phase's `[dry-run] Would embed ...`
+  // summary must not leak onto stdout ahead of the JSON CycleReport.
+  test('--dry-run --json emits only JSON even when embed has stale chunks', async () => {
+    await engine.putPage('concepts/testing', {
+      type: 'concept',
+      title: 'Testing',
+      compiled_truth: 'Testing keeps JSON contracts honest.',
+      timeline: '',
+    });
+    await engine.upsertChunks('concepts/testing', [
+      { chunk_index: 0, chunk_text: 'Testing keeps JSON contracts honest.', chunk_source: 'compiled_truth' },
+    ]);
+
+    const lines: string[] = [];
+    const logSpy = spyOn(console, 'log').mockImplementation((msg: string) => { lines.push(String(msg)); });
+    await runDream(engine, ['--dir', repo, '--phase', 'embed', '--dry-run', '--json']);
+    logSpy.mockRestore();
+
+    const output = lines.join('\n');
+    expect(output.trimStart().startsWith('{')).toBe(true);
+    const parsed = JSON.parse(output);
+    expect(parsed.schema_version).toBe('1');
+    expect(parsed.phases[0].phase).toBe('embed');
+    // The stale chunk was still counted in the structured report.
+    expect(parsed.phases[0].details.would_embed).toBe(1);
+  });
+
   test('human output for clean status mentions "Brain is healthy"', async () => {
     const lines: string[] = [];
     const logSpy = spyOn(console, 'log').mockImplementation((msg: string) => { lines.push(String(msg)); });

test/list-pages-offset.test.ts

@@ -1,55 +0,0 @@
-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);
-  });
-});