fix(onboard): stop dropping onboard-check remediations on the --apply --auto path

Takeover of #2161. runRemediation ignored onboard-check extras in three
places: the pre-flight plan, the initial recommendation build, and the D7
mid-run recheck that rebuilds recs after every completed step. The --check
path threaded extras correctly, so `gbrain onboard --apply --auto` reported
"Nothing to do" when the only remediable work came from onboard checks —
and even with the first two sites fixed (the original PR diff), any plan
with 2+ steps dropped all remaining extras after step 1 via the recheck.

- Add RemediationOpts.extraRemediations; thread it through the pre-flight
  plan, initial recs, and the mid-run recheck.
- Recheck filters extras to ids not already processed this run: extras
  carry static status:'remediable', so unfiltered threading would resubmit
  completed extras forever.
- Wire the CLI --auto path (onboard.ts) AND the MCP run_onboard auto path
  (operations.ts), which already computed the scope-filtered allowedExtras
  and then dropped it.
- Regression test: extras-only plan on an empty brain runs BOTH extras
  exactly once and terminates (serial file: mock.module queue stub +
  GBRAIN_HOME tmpdir).

Co-authored-by: brettdavies <brettdavies@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/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/commands/onboard.ts

@@ -142,12 +142,16 @@ export async function runOnboard(engine: BrainEngine, args: string[]): Promise<v
 
   // --auto path: runs through the T2 library orchestrator. Hooks emit CLI
   // progress to stderr; the final result lands as JSON on stdout (or human
-  // summary).
+  // summary). extraRemediations (gathered above from runAllOnboardChecks)
+  // is threaded into the runner so the onboard-check remediations
+  // (extract-ner, extract-timeline-from-meetings, etc.) reach the planner
+  // — the same wiring the --check path uses above.
   const result = await runRemediation(
     engine,
     {
       targetScore,
       maxUsd,
+      extraRemediations,
       // --auto --yes opts into the prompt_required tier too; library
       // doesn't distinguish auto_apply vs prompt_required, it just runs
       // every remediation in the plan. The plan-building side (T12 render)

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',

src/core/operations.ts

@@ -4957,7 +4957,7 @@ const run_onboard: Operation = {
     // typo, the underlying queue.add would reject. Defense-in-depth.
     const result = await runRemediation(
       ctx.engine,
-      { targetScore, maxUsd },
+      { targetScore, maxUsd, extraRemediations: allowedExtras },
       {},
     );
 

src/core/remediation/run.ts

@@ -66,9 +66,10 @@ export async function runRemediation(
   } = await import('../remediation-checkpoint.ts');
 
   const ctx = await loadRecommendationContext(engine);
+  const extraRemediations = opts.extraRemediations ?? [];
 
   // Pre-flight ceiling check via the shared plan computation.
-  const initialPlan = await computeRemediationPlan(engine, { targetScore });
+  const initialPlan = await computeRemediationPlan(engine, { targetScore, extraRemediations });
   if (initialPlan.target_unreachable) {
     hooks.onTargetUnreachable?.(targetScore, initialPlan.max_reachable_score);
     return {
@@ -87,7 +88,7 @@ export async function runRemediation(
   }
 
   const initialHealth = await engine.getHealth();
-  let recs: RemediationStep[] = computeRecommendations(initialHealth, ctx)
+  let recs: RemediationStep[] = computeRecommendations(initialHealth, ctx, extraRemediations)
     .filter((r) => r.status === 'remediable');
   if (recs.length === 0) {
     hooks.onNothingToDo?.(initialHealth.brain_score, targetScore);
@@ -305,7 +306,13 @@ export async function runRemediation(
       // steps with bumped retry suffix (D1).
       if (recs.length === 0 || stepCount >= maxJobs) break;
       const freshHealth = await engine.getHealth();
-      recs = computeRecommendations(freshHealth, ctx).filter((r) => r.status === 'remediable');
+      // Extras carry a static status:'remediable' — a fresh health snapshot
+      // never ages them out the way health-derived steps drop. Filter out
+      // ids this run already processed (any terminal status), or the recheck
+      // would resubmit completed extras every iteration, forever.
+      const processedIds = new Set(submitted.map((s) => s.id));
+      const pendingExtras = extraRemediations.filter((r) => !processedIds.has(r.id));
+      recs = computeRecommendations(freshHealth, ctx, pendingExtras).filter((r) => r.status === 'remediable');
     }
   };
 

src/core/remediation/types.ts

@@ -63,6 +63,16 @@ export interface RemediationOpts {
   resumePlanHash?: string;
   /** Whether to attempt resume at all (default false). */
   resume?: boolean;
+  /**
+   * Caller-supplied RemediationStep entries threaded into the planner.
+   * Mirrors RemediationPlanOpts.extraRemediations so onboard's --apply
+   * --auto path (and MCP run_onboard auto modes) forward the same
+   * onboard-check remediations the --check path already passes through
+   * computeRemediationPlan. Without this the runner saw only generic
+   * brain_score remediations and reported "Nothing to do" whenever the
+   * only applicable work was an extra (e.g. extract-ner).
+   */
+  extraRemediations?: RemediationStep[];
 }
 
 /**

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);
-});

test/remediation-run-extras.serial.test.ts

@@ -0,0 +1,108 @@
+// test/remediation-run-extras.serial.test.ts
+// Regression for PR #2161 takeover: `gbrain onboard --apply --auto` dropped
+// onboard-check extraRemediations. Two distinct halves of the bug:
+//   1. runRemediation built the pre-flight plan + initial recs WITHOUT the
+//      extras, so an extras-only plan reported "Nothing to do".
+//   2. The D7 mid-run recheck rebuilt recs WITHOUT the extras after every
+//      completed step, so with 2+ plannable steps all remaining extras were
+//      dropped after step 1. The recheck must also filter out extras this
+//      run already processed — extras carry static status:'remediable', so
+//      unfiltered threading would resubmit completed extras forever.
+//
+// SERIAL: mock.module (queue + wait-for-completion stubs, R2) + GBRAIN_HOME
+// env mutation so checkpoint files land in a tmpdir, not ~/.gbrain.
+
+import { describe, expect, test, beforeAll, afterAll, mock } from 'bun:test';
+import { mkdtempSync, rmSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { makeRemediationStep } from '../src/core/remediation-step.ts';
+
+// Stub the Minion queue: every submitted job is immediately 'completed'.
+// runRemediation only calls queue.add + waitForCompletion(queue, id).
+let nextJobId = 1;
+const submittedJobs: Array<{ name: string }> = [];
+mock.module('../src/core/minions/queue.ts', () => ({
+  MinionQueue: class {
+    async add(name: string) {
+      submittedJobs.push({ name });
+      return { id: nextJobId++, status: 'completed' };
+    }
+  },
+}));
+mock.module('../src/core/minions/wait-for-completion.ts', () => ({
+  waitForCompletion: async () => ({ status: 'completed' }),
+}));
+
+let engine: PGLiteEngine;
+let home: string;
+const prevHome = process.env.GBRAIN_HOME;
+
+beforeAll(async () => {
+  home = mkdtempSync(join(tmpdir(), 'gbrain-remextras-'));
+  process.env.GBRAIN_HOME = home;
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+}, 120_000);
+
+afterAll(async () => {
+  await engine.disconnect();
+  if (prevHome === undefined) delete process.env.GBRAIN_HOME;
+  else process.env.GBRAIN_HOME = prevHome;
+  rmSync(home, { recursive: true, force: true });
+});
+
+function extra(id: string, job: string) {
+  return makeRemediationStep({
+    id,
+    job,
+    params: {},
+    severity: 'medium',
+    est_seconds: 5,
+    est_usd_cost: 0,
+    rationale: 'synthetic onboard-check extra',
+    status: 'remediable',
+  });
+}
+
+describe('runRemediation extraRemediations threading', () => {
+  test('extras-only plan runs BOTH extras and terminates (no Nothing-to-do, no resubmit loop)', async () => {
+    // Empty PGLite brain → zero health-derived recommendations. Without the
+    // fix, half 1 makes this run return submitted: [] via onNothingToDo.
+    // With only half 1 (the original PR #2161 diff), the mid-run recheck
+    // drops the second extra after step 1 — submitted has 1 entry, not 2.
+    const { runRemediation } = await import('../src/core/remediation/run.ts');
+    let nothingToDo = false;
+    const result = await runRemediation(
+      engine,
+      {
+        targetScore: 1,
+        extraRemediations: [
+          extra('onboard.extract_ner', 'extract-ner'),
+          extra('onboard.extract_timeline', 'extract-timeline-from-meetings'),
+        ],
+        // Safety bound: an unfiltered recheck would resubmit completed
+        // extras forever; maxJobs turns that regression into a fast fail
+        // (extra count > 1 below) instead of a hung test.
+        maxJobs: 5,
+      },
+      { onNothingToDo: () => { nothingToDo = true; } },
+    );
+
+    expect(nothingToDo).toBe(false);
+    const ids = result.submitted.map((s) => s.id);
+    expect(ids).toContain('onboard.extract_ner');
+    expect(ids).toContain('onboard.extract_timeline');
+    // Each extra ran exactly once — the recheck must not re-plan extras the
+    // run already processed.
+    expect(ids.filter((i) => i === 'onboard.extract_ner').length).toBe(1);
+    expect(ids.filter((i) => i === 'onboard.extract_timeline').length).toBe(1);
+    expect(result.submitted.every((s) => s.status === 'completed')).toBe(true);
+    expect(submittedJobs.map((j) => j.name).sort()).toEqual([
+      'extract-ner',
+      'extract-timeline-from-meetings',
+    ]);
+  });
+});