fix(backlinks): honor positional check-backlinks directory argument

The help text (gbrain check-backlinks <check|fix> [dir]) promised a
positional directory argument, but runBacklinks only parsed --dir and
defaulted to cwd, so the walker ran from the wrong root and could hit
EPERM on unreadable sibling dirs.

Extract parseBacklinksArgs: positional [dir] is now honored, --dir still
overrides it, --dry-run preserved, and a --dir flag missing its value
falls back to the positional dir instead of picking up undefined.

Takeover of #852 (rebased onto master past the findBacklinkGaps dedupe
test block). Fixes #485.

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/backlinks.ts

@@ -5,8 +5,8 @@
  * checks if back-links exist, and optionally creates them.
  *
  * Usage:
- *   gbrain check-backlinks check [--dir <brain-dir>]     # report missing back-links
- *   gbrain check-backlinks fix [--dir <brain-dir>]        # create missing back-links
+ *   gbrain check-backlinks check [dir] [--dir <brain-dir>] # report missing back-links
+ *   gbrain check-backlinks fix [dir] [--dir <brain-dir>]   # create missing back-links
  *   gbrain check-backlinks fix --dry-run                  # preview fixes
  */
 
@@ -201,6 +201,40 @@ export interface BacklinksResult {
   dryRun: boolean;
 }
 
+export interface ParsedBacklinksArgs {
+  subcommand: string | undefined;
+  brainDir: string;
+  dryRun: boolean;
+}
+
+export function parseBacklinksArgs(args: string[]): ParsedBacklinksArgs {
+  const subcommand = args[0];
+  const dryRun = args.includes('--dry-run');
+  const dirIdx = args.indexOf('--dir');
+  const flagDir = dirIdx >= 0 && args[dirIdx + 1] && !args[dirIdx + 1].startsWith('--')
+    ? args[dirIdx + 1]
+    : undefined;
+
+  let positionalDir: string | undefined;
+  for (let i = 1; i < args.length; i++) {
+    const arg = args[i];
+    if (arg === '--dir') {
+      i++;
+      continue;
+    }
+    if (arg === '--dry-run') continue;
+    if (arg.startsWith('--')) continue;
+    positionalDir = arg;
+    break;
+  }
+
+  return {
+    subcommand,
+    brainDir: flagDir ?? positionalDir ?? '.',
+    dryRun,
+  };
+}
+
 /**
  * Library-level backlinks check/fix. Throws on validation errors; returns a
  * structured result so Minions handlers + autopilot-cycle can surface counts.
@@ -236,16 +270,14 @@ export async function runBacklinksCore(opts: BacklinksOpts): Promise<BacklinksRe
 }
 
 export async function runBacklinks(args: string[]) {
-  const subcommand = args[0];
-  const dirIdx = args.indexOf('--dir');
-  const brainDir = dirIdx >= 0 ? args[dirIdx + 1] : '.';
-  const dryRun = args.includes('--dry-run');
+  const { subcommand, brainDir, dryRun } = parseBacklinksArgs(args);
 
   if (!subcommand || !['check', 'fix'].includes(subcommand)) {
-    console.error('Usage: gbrain check-backlinks <check|fix> [--dir <brain-dir>] [--dry-run]');
+    console.error('Usage: gbrain check-backlinks <check|fix> [dir] [--dir <brain-dir>] [--dry-run]');
     console.error('  check    Report missing back-links');
     console.error('  fix      Create missing back-links (appends to Timeline)');
-    console.error('  --dir    Brain directory (default: current directory)');
+    console.error('  dir      Brain directory (default: current directory)');
+    console.error('  --dir    Brain directory override');
     console.error('  --dry-run  Preview fixes without writing');
     process.exit(1);
   }

src/core/operations.ts

@@ -769,7 +769,7 @@ const get_page: Operation = {
 
 const put_page: Operation = {
   name: 'put_page',
-  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. 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/backlinks.test.ts

@@ -4,6 +4,7 @@ import {
   extractPageTitle,
   hasBacklink,
   buildBacklinkEntry,
+  parseBacklinksArgs,
 } from '../src/commands/backlinks.ts';
 
 describe('extractEntityRefs', () => {
@@ -104,3 +105,26 @@ describe('findBacklinkGaps dedupe (v0.36.x #967 regression)', () => {
     }
   });
 });
+
+describe('parseBacklinksArgs', () => {
+  test('uses positional dir for check and fix subcommands', () => {
+    expect(parseBacklinksArgs(['check', '/tmp/brain']).brainDir).toBe('/tmp/brain');
+    expect(parseBacklinksArgs(['fix', '/tmp/brain']).brainDir).toBe('/tmp/brain');
+  });
+
+  test('defaults to cwd when no dir given', () => {
+    expect(parseBacklinksArgs(['check']).brainDir).toBe('.');
+  });
+
+  test('--dir overrides positional dir and preserves dry-run', () => {
+    const parsed = parseBacklinksArgs(['fix', '/tmp/ignored', '--dir', '/tmp/brain', '--dry-run']);
+    expect(parsed.subcommand).toBe('fix');
+    expect(parsed.brainDir).toBe('/tmp/brain');
+    expect(parsed.dryRun).toBe(true);
+  });
+
+  test('--dir missing its value falls back to positional dir', () => {
+    expect(parseBacklinksArgs(['check', '/tmp/brain', '--dir']).brainDir).toBe('/tmp/brain');
+    expect(parseBacklinksArgs(['check', '--dir', '--dry-run']).brainDir).toBe('.');
+  });
+});

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/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);
-  });
-});