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/guides/live-sync.md

@@ -21,17 +21,14 @@ GBrain is tuned for the Supabase **Transaction pooler** (port 6543): it
 auto-disables prepared statements there and routes `engine.transaction()`
 (migrations, DDL, sync imports) to a derived **direct** connection
 (`db.<ref>.supabase.co:5432`). That direct host is IPv6-only, so on an
-IPv4-only host it is unreachable. When that happens gbrain now falls back to
-the pooler automatically (one stderr warning, then single-pool mode for the
-rest of the process) — but the pooler's ~2-min statement timeout can truncate
-very long migrations or bulk imports.
+IPv4-only host, reads work but sync **silently skips most pages**. This is the
+number one cause of "sync ran but nothing happened."
 
 Fix: make the direct connection reachable over IPv4. Either set
 `GBRAIN_DIRECT_DATABASE_URL` to the **Session pooler** string (port 5432 on the
-`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on.
-`GBRAIN_DISABLE_DIRECT_POOL=1` skips the direct pool (and the fallback warning)
-entirely. Verify by running `gbrain sync` and checking that the page count in
-`gbrain stats` matches the syncable file count in the repo.
+`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on. Verify by
+running `gbrain sync` and checking that the page count in `gbrain stats` matches
+the syncable file count in the repo.
 
 ### The Primitives
 

llms-full.txt

@@ -2720,17 +2720,14 @@ GBrain is tuned for the Supabase **Transaction pooler** (port 6543): it
 auto-disables prepared statements there and routes `engine.transaction()`
 (migrations, DDL, sync imports) to a derived **direct** connection
 (`db.<ref>.supabase.co:5432`). That direct host is IPv6-only, so on an
-IPv4-only host it is unreachable. When that happens gbrain now falls back to
-the pooler automatically (one stderr warning, then single-pool mode for the
-rest of the process) — but the pooler's ~2-min statement timeout can truncate
-very long migrations or bulk imports.
+IPv4-only host, reads work but sync **silently skips most pages**. This is the
+number one cause of "sync ran but nothing happened."
 
 Fix: make the direct connection reachable over IPv4. Either set
 `GBRAIN_DIRECT_DATABASE_URL` to the **Session pooler** string (port 5432 on the
-`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on.
-`GBRAIN_DISABLE_DIRECT_POOL=1` skips the direct pool (and the fallback warning)
-entirely. Verify by running `gbrain sync` and checking that the page count in
-`gbrain stats` matches the syncable file count in the repo.
+`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on. Verify by
+running `gbrain sync` and checking that the page count in `gbrain stats` matches
+the syncable file count in the repo.
 
 ### The Primitives
 

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/commands/init.ts

@@ -1078,9 +1078,6 @@ async function initPostgres(opts: {
     console.warn('  Direct connections are IPv6 only and fail in many environments.');
     console.warn('  Use the Transaction pooler connection string instead (port 6543):');
     console.warn('  Supabase Dashboard > Connect (top bar) > Connection String > Transaction pooler');
-    console.warn('  (With a pooler URL, gbrain derives a direct connection for DDL and falls back');
-    console.warn('  to the pooler automatically if that host is unreachable. Power users:');
-    console.warn('  GBRAIN_DIRECT_DATABASE_URL overrides the derived URL; GBRAIN_DISABLE_DIRECT_POOL=1 disables it.)');
     console.warn('');
   }
 
@@ -1094,9 +1091,6 @@ async function initPostgres(opts: {
       if (databaseUrl.includes('supabase.co') && (msg.includes('ECONNREFUSED') || msg.includes('ETIMEDOUT'))) {
         console.error('Connection failed. Supabase direct connections (db.*.supabase.co:5432) are IPv6 only.');
         console.error('Use the Transaction pooler connection string instead (port 6543).');
-        console.error('(gbrain derives its own direct connection from pooler URLs for DDL; if that host is');
-        console.error('unreachable it falls back to the pooler. GBRAIN_DIRECT_DATABASE_URL overrides the');
-        console.error('derived URL; GBRAIN_DISABLE_DIRECT_POOL=1 disables the direct pool entirely.)');
       }
       throw e;
     }

src/core/connection-manager.ts

@@ -167,25 +167,6 @@ export function deriveDirectUrl(url: string): string | null {
   }
 }
 
-/**
- * Error codes that mean "the direct host is unreachable from this network"
- * (#1641). The auto-derived db.<ref>.supabase.co host is IPv6-only without
- * the paid IPv4 add-on, so ENOTFOUND/ECONNREFUSED here is expected on
- * IPv4-only networks — we fall back to the pooler instead of failing init.
- */
-const NETWORK_UNREACHABLE_CODES = [
-  'ENOTFOUND', 'ECONNREFUSED', 'ENETUNREACH', 'EHOSTUNREACH',
-  'ETIMEDOUT', 'CONNECT_TIMEOUT',
-];
-
-/** True when err looks like a network-unreachable failure (not auth/SQL). */
-export function isNetworkUnreachableError(err: unknown): boolean {
-  const code = (err as { code?: unknown } | null)?.code;
-  if (typeof code === 'string' && NETWORK_UNREACHABLE_CODES.includes(code)) return true;
-  const msg = err instanceof Error ? err.message : String(err);
-  return NETWORK_UNREACHABLE_CODES.some(c => msg.includes(c));
-}
-
 /**
  * Read kill-switch state from env. Subordinate to parent manager's state
  * when present (A2 inheritance).
@@ -338,30 +319,7 @@ export class ConnectionManager {
         throw err;
       });
     }
-    let pool: Sql | null;
-    try {
-      pool = await this._directInit;
-    } catch (err) {
-      // #1641: the derived direct host (db.<ref>.supabase.co) is IPv6-only
-      // without Supabase's IPv4 add-on. On IPv4-only networks the direct
-      // pool can never connect — permanently fall back to the read pool
-      // (self-activating kill-switch) instead of failing init/migrations.
-      // Non-network errors (auth, SQL) still throw: they mean misconfig,
-      // not unreachability.
-      if (isNetworkUnreachableError(err)) {
-        const alreadyWarned = this._killSwitch;
-        this._killSwitch = true;
-        const msg = err instanceof Error ? err.message : String(err);
-        if (!alreadyWarned) console.error(
-          `gbrain: direct connection to ${this._directUrl ? this.hostOnly(this._directUrl) : 'unknown host'} unreachable (${msg}); ` +
-          'falling back to the pooler for DDL/bulk (long migrations may hit the pooler statement timeout). ' +
-          'Set GBRAIN_DIRECT_DATABASE_URL to a reachable direct URL (e.g. the Session pooler, port 5432) or enable the Supabase IPv4 add-on; ' +
-          'GBRAIN_DISABLE_DIRECT_POOL=1 silences this.',
-        );
-        return this.getReadPool();
-      }
-      throw err;
-    }
+    const pool = await this._directInit;
     if (!pool) {
       // Defensive — initDirectPool should have thrown.
       throw new Error('connection-manager: direct pool init returned null');
@@ -392,9 +350,8 @@ export class ConnectionManager {
       },
     };
     const t0 = Date.now();
-    let pool: Sql | null = null;
     try {
-      pool = postgres(this._directUrl, opts);
+      const pool = postgres(this._directUrl, opts);
       // Probe to validate connectivity early.
       await pool`SELECT 1`;
       logConnectionEvent({
@@ -405,9 +362,6 @@ export class ConnectionManager {
       });
       return pool;
     } catch (err) {
-      // Don't leak the failed pool's sockets/timers (#1641 fallback keeps
-      // the process running afterward).
-      if (pool) await endPoolBounded(pool);
       logConnectionEvent({
         pool: 'ddl',
         op: 'error',

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/connection-manager.serial.test.ts

@@ -3,7 +3,6 @@ import {
   isSupabasePoolerUrl,
   deriveDirectUrl,
   readKillSwitchEnv,
-  isNetworkUnreachableError,
   resolveDirectPoolSize,
   ConnectionManager,
   DEFAULT_DIRECT_POOL_SIZE,
@@ -239,65 +238,3 @@ describe('ConnectionManager — parent inheritance (A2)', () => {
     }
   });
 });
-
-describe('isNetworkUnreachableError (#1641)', () => {
-  test('classifies network codes as unreachable', () => {
-    for (const code of ['ENOTFOUND', 'ECONNREFUSED', 'ENETUNREACH', 'EHOSTUNREACH', 'ETIMEDOUT', 'CONNECT_TIMEOUT']) {
-      const err = Object.assign(new Error('connect failed'), { code });
-      expect(isNetworkUnreachableError(err)).toBe(true);
-    }
-  });
-
-  test('classifies by message when code absent', () => {
-    expect(isNetworkUnreachableError(new Error('getaddrinfo ENOTFOUND db.abc.supabase.co'))).toBe(true);
-  });
-
-  test('auth/SQL errors are NOT unreachable', () => {
-    expect(isNetworkUnreachableError(new Error('password authentication failed for user "postgres"'))).toBe(false);
-    expect(isNetworkUnreachableError(new Error('syntax error at or near "SELEC"'))).toBe(false);
-    expect(isNetworkUnreachableError(null)).toBe(false);
-  });
-});
-
-describe('ConnectionManager — direct-pool fallback on unreachable host (#1641)', () => {
-  let originalKillSwitch: string | undefined;
-  let originalError: typeof console.error;
-  let errLines: string[];
-  beforeEach(() => {
-    originalKillSwitch = process.env.GBRAIN_DISABLE_DIRECT_POOL;
-    delete process.env.GBRAIN_DISABLE_DIRECT_POOL;
-    originalError = console.error;
-    errLines = [];
-    console.error = (...args: unknown[]) => { errLines.push(args.join(' ')); };
-  });
-  afterEach(() => {
-    console.error = originalError;
-    if (originalKillSwitch === undefined) delete process.env.GBRAIN_DISABLE_DIRECT_POOL;
-    else process.env.GBRAIN_DISABLE_DIRECT_POOL = originalKillSwitch;
-  });
-
-  test('ddl() falls back to the read pool when the direct host is unreachable', async () => {
-    const cm = new ConnectionManager({
-      url: 'postgresql://postgres.abc:p@aws.pooler.supabase.com:6543/db',
-      // 127.0.0.1:9 (discard) → instant ECONNREFUSED, the IPv4-only-network shape.
-      directUrl: 'postgresql://postgres:p@127.0.0.1:9/db',
-    });
-    const fakeReadPool = {} as ReturnType<typeof ConnectionManager.prototype.read>;
-    cm.setReadPool(fakeReadPool);
-    expect(cm.isDualPoolActive()).toBe(true);
-
-    const pool = await cm.ddl(); // without the fix this throws ECONNREFUSED
-    expect(pool).toBe(fakeReadPool);
-    // Self-activating kill-switch: subsequent calls skip the direct pool.
-    expect(cm.isKillSwitchActive()).toBe(true);
-    expect(cm.isDualPoolActive()).toBe(false);
-    expect(cm.describeMode().mode).toBe('single (kill-switch)');
-    // One stderr line mentioning the power-user override.
-    const warning = errLines.filter(l => l.includes('GBRAIN_DIRECT_DATABASE_URL'));
-    expect(warning.length).toBe(1);
-
-    const again = await cm.ddl();
-    expect(again).toBe(fakeReadPool);
-    expect(errLines.filter(l => l.includes('GBRAIN_DIRECT_DATABASE_URL')).length).toBe(1);
-  }, 20000);
-});