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

@@ -24,7 +24,6 @@ import type { GBrainConfig } from './core/config.ts';
 import type { AIGatewayConfig } from './core/ai/types.ts';
 import type { BrainEngine } from './core/engine.ts';
 import { operations, OperationError } from './core/operations.ts';
-import { resolveSourceIdEngineFree } from './core/source-resolver.ts';
 import { formatVolunteeredPage } from './core/context/volunteer.ts';
 import type { Operation, OperationContext } from './core/operations.ts';
 import { shouldForceExitAfterMain, finishCliTeardown, flushThenExit, currentExitCode, setCliExitVerdict } from './core/cli-force-exit.ts';
@@ -383,15 +382,6 @@ async function main() {
     if (op.localOnly) {
       refuseThinClient(command, cfgPre!.remote_mcp!.mcp_url);
     }
-    // #2098: the local path resolves --source / GBRAIN_SOURCE / .gbrain-source
-    // inside makeContext (ctx.sourceId), which this route never reaches — so
-    // scope must be mapped onto the op's source_id wire param before the call.
-    try {
-      applyThinClientSourceScope(op, params);
-    } catch (e: unknown) {
-      console.error(e instanceof Error ? e.message : String(e));
-      process.exit(1);
-    }
     await runThinClientRouted(op, params, cfgPre!, cliOpts);
     return;
   }
@@ -474,7 +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`
@@ -557,7 +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) {
@@ -767,10 +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];
@@ -784,12 +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++];
@@ -798,10 +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);
@@ -812,60 +877,6 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
   return params;
 }
 
-/**
- * #2098: thin-client source scoping. Locally, --source / GBRAIN_SOURCE /
- * .gbrain-source resolve to ctx.sourceId in makeContext; the thin-client
- * route short-circuits before that, so `gbrain query --source X` against a
- * remote brain silently searched unscoped. This runs the engine-free tiers
- * (flag → env → dotfile; the DB-backed tiers can't run without an engine —
- * the server's grant scoping covers the rest) and maps the result onto the
- * op's `source_id` wire param.
- *
- * Ops that declare their OWN `source` param (facts add, etc.) are left
- * untouched — their --source is an op param, not scope. An explicit --source
- * on an op with no source_id wire param throws (loud beats silent drop);
- * ambient env/dotfile scope with nowhere to send it is ignored, matching the
- * pre-fix behavior for non-scopeable ops. Exported for tests.
- */
-// Ops whose `source_id` wire param is NOT read-scope semantics: get_skill's
-// source_id flips the lookup from host catalog to brain-resident-pack
-// (getResidentSkillDetail). Ambient env/dotfile scope must never leak into
-// these; an explicit --source-id still passes through untouched above.
-const NON_SCOPE_SOURCE_ID_OPS = new Set(['get_skill']);
-
-export function applyThinClientSourceScope(
-  op: Operation,
-  params: Record<string, unknown>,
-  cwd?: string,
-): void {
-  if ('source' in op.params) return; // the op owns --source; not a scope flag
-  const explicit = typeof params.source === 'string' && params.source.length > 0
-    ? (params.source as string)
-    : null;
-  delete params.source; // never a wire param on these ops — don't leak it
-  // Explicit per-call scope already on the wire wins over ambient tiers.
-  if (params.source_id !== undefined || params.all_sources === true) {
-    if (explicit) {
-      throw new Error('Pass either --source or --source-id/--all-sources, not both.');
-    }
-    return;
-  }
-  const resolved = resolveSourceIdEngineFree(explicit, cwd);
-  if (!resolved) return;
-  if (!('source_id' in op.params) || NON_SCOPE_SOURCE_ID_OPS.has(op.name)) {
-    if (explicit) {
-      const hint = NON_SCOPE_SOURCE_ID_OPS.has(op.name)
-        ? `(its source_id parameter is not a scope filter; pass --source-id explicitly if you mean it)`
-        : `(the remote op has no source_id parameter; the server scopes it to your grant)`;
-      throw new Error(
-        `gbrain ${op.cliHints?.name || op.name} does not accept --source on a thin-client install ${hint}.`,
-      );
-    }
-    return; // ambient env/dotfile scope with nowhere to send it
-  }
-  params.source_id = resolved;
-}
-
 async function makeContext(engine: BrainEngine, params: Record<string, unknown>): Promise<OperationContext> {
   // v0.31.8 (D11): resolve sourceId via the canonical 6-tier chain. Honors
   // --source / GBRAIN_SOURCE / .gbrain-source / path-match / brain default /
@@ -2317,6 +2328,10 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${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/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/source-resolver.ts

@@ -160,33 +160,6 @@ export async function resolveSourceId(
   return 'default';
 }
 
-/**
- * Engine-free tiers (1-3) of the resolution chain: explicit flag →
- * GBRAIN_SOURCE env → .gbrain-source dotfile walk. Used by the thin-client
- * CLI path (#2098), which has no local engine to run tiers 4-6 or
- * assertSourceExists against — the remote server enforces existence + grant.
- * Returns null when no engine-free tier fires.
- */
-export function resolveSourceIdEngineFree(
-  explicit: string | null | undefined,
-  cwd: string = process.cwd(),
-): string | null {
-  if (explicit) {
-    if (!SOURCE_ID_RE.test(explicit)) {
-      throw new Error(`Invalid --source value "${explicit}". Must match [a-z0-9-]{1,32}.`);
-    }
-    return explicit;
-  }
-  const env = process.env.GBRAIN_SOURCE;
-  if (env && env.length > 0) {
-    if (!SOURCE_ID_RE.test(env)) {
-      throw new Error(`Invalid GBRAIN_SOURCE value "${env}". Must match [a-z0-9-]{1,32}.`);
-    }
-    return env;
-  }
-  return readDotfileWalk(cwd);
-}
-
 /**
  * Returns the id of the SINGLE registered non-default source with a
  * local_path, when exactly one such row exists. Returns null when:

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/thin-client-source-scope.test.ts

@@ -1,142 +0,0 @@
-/**
- * #2098: thin-client routing dropped --source / GBRAIN_SOURCE / .gbrain-source.
- *
- * The local CLI path resolves source scope in makeContext (ctx.sourceId); the
- * thin-client route short-circuits before that and sent params verbatim, so
- * `gbrain query --source X` against a remote brain silently searched unscoped
- * (the server op ignores the unknown `source` key).
- *
- * applyThinClientSourceScope runs the engine-free tiers (flag → env → dotfile)
- * and maps the result onto the op's `source_id` wire param. These tests fail
- * without the fix (params.source_id stays undefined / params.source leaks).
- */
-
-import { describe, test, expect } from 'bun:test';
-import { mkdtempSync, rmSync, writeFileSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import { applyThinClientSourceScope, parseOpArgs } from '../src/cli.ts';
-import { operationsByName } from '../src/core/operations.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-const queryOp = operationsByName.query;
-
-describe('applyThinClientSourceScope (#2098)', () => {
-  test('--source maps onto the query op wire param source_id', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['find things', '--source', 'wiki']);
-      expect(params.source).toBe('wiki'); // pre-fix state: wrong key
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBe('wiki');
-      expect('source' in params).toBe(false); // never leaks the unknown key
-    });
-  });
-
-  test('GBRAIN_SOURCE env tier fires when no flag is passed', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
-      const params = parseOpArgs(queryOp, ['find things']);
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBe('gstack');
-    });
-  });
-
-  test('.gbrain-source dotfile tier fires when flag and env are absent', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const tmp = mkdtempSync(join(tmpdir(), 'gbrain-thin-scope-'));
-      try {
-        writeFileSync(join(tmp, '.gbrain-source'), 'essays\n');
-        const params = parseOpArgs(queryOp, ['find things']);
-        applyThinClientSourceScope(queryOp, params, tmp);
-        expect(params.source_id).toBe('essays');
-      } finally {
-        rmSync(tmp, { recursive: true, force: true });
-      }
-    });
-  });
-
-  test('explicit --source-id on the wire wins over ambient env scope', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
-      const params = parseOpArgs(queryOp, ['find things', '--source-id', 'wiki']);
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBe('wiki');
-    });
-  });
-
-  test('--source together with --source-id is rejected loudly', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['q', '--source', 'a', '--source-id', 'b']);
-      expect(() => applyThinClientSourceScope(queryOp, params, '/')).toThrow(/not both/);
-    });
-  });
-
-  test('invalid --source value is rejected loudly', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['q', '--source', 'Bad_Value!']);
-      expect(() => applyThinClientSourceScope(queryOp, params, '/')).toThrow(/Invalid --source/);
-    });
-  });
-
-  test('--source on an op with no source_id wire param errors instead of silently dropping', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const op = operationsByName.add_tag;
-      expect('source_id' in op.params).toBe(false);
-      const params = { slug: 'x', tag: 'y', source: 'wiki' };
-      expect(() => applyThinClientSourceScope(op, params, '/')).toThrow(/--source/);
-    });
-  });
-
-  test('ambient env scope on an op with no source_id wire param is ignored (no throw)', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'wiki' }, () => {
-      const op = operationsByName.add_tag;
-      const params: Record<string, unknown> = { slug: 'x', tag: 'y' };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source_id).toBeUndefined();
-    });
-  });
-
-  test('ops that declare their OWN source param are left untouched', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const op = operationsByName.put_raw_data;
-      expect('source' in op.params).toBe(true);
-      const params: Record<string, unknown> = { slug: 'x', source: 'crustdata', data: {} };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source).toBe('crustdata');
-      expect(params.source_id).toBeUndefined();
-    });
-  });
-
-  test('get_skill: ambient scope never leaks into its non-scope source_id param', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'wiki' }, () => {
-      const op = operationsByName.get_skill;
-      expect('source_id' in op.params).toBe(true); // has the param, but it is a mode switch
-      const params: Record<string, unknown> = { name: 'ingest' };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source_id).toBeUndefined(); // would flip host catalog → brain-pack lookup
-    });
-  });
-
-  test('get_skill: explicit --source errors instead of masquerading as --source-id', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const op = operationsByName.get_skill;
-      const params: Record<string, unknown> = { name: 'ingest', source: 'wiki' };
-      expect(() => applyThinClientSourceScope(op, params, '/')).toThrow(/--source-id/);
-    });
-  });
-
-  test('get_skill: explicit --source-id passes through untouched', async () => {
-    await withEnv({ GBRAIN_SOURCE: 'gstack' }, () => {
-      const op = operationsByName.get_skill;
-      const params: Record<string, unknown> = { name: 'ingest', source_id: 'wiki' };
-      applyThinClientSourceScope(op, params, '/');
-      expect(params.source_id).toBe('wiki');
-    });
-  });
-
-  test('no scope from any tier leaves params unchanged', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () => {
-      const params = parseOpArgs(queryOp, ['find things']);
-      applyThinClientSourceScope(queryOp, params, '/');
-      expect(params.source_id).toBeUndefined();
-    });
-  });
-});