fix(upgrade): post-upgrade auto-applies pending schema migrations (X1)

Prior behavior: `gbrain upgrade` → `gbrain post-upgrade` → `apply-migrations`
only WARNs at apply-migrations.ts:296-302 when schema version is behind
LATEST_VERSION, telling the user to run `gbrain init --migrate-only`. 11
wedge incidents over 2 years have proven users don't read that WARN —
they file an issue instead.

This commit makes `runPostUpgrade` explicitly call `engine.initSchema()`
after the orchestrator migration pass, mirroring `init --migrate-only`'s
flow. Side-effect: `gbrain upgrade` now walks away with a healthy brain
in the cluster A wedge case (#670, #661, #657, #651, #625, #615, #609).

Defensive: wrapped in try/catch so a connection or DDL failure falls
back to the existing user-facing WARN. The hint to run
`gbrain init --migrate-only` is preserved as the manual escape hatch.

Pairs with v0.28.5's A1 (hasPendingMigrations probe in connectEngine):
the upgrade path runs initSchema explicitly here, while every other code
path that goes through connectEngine gets the cheap probe.

Codex outside-voice review caught this gap during plan review: "the plan
still does not prove `upgrade` will actually run schema migrations."
This is the load-bearing fix that makes v0.28.5's headline outcome
("run upgrade, brain works") literally true for cluster A.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/commands/upgrade.ts

@@ -218,6 +218,37 @@ export async function runPostUpgrade(args: string[] = []): Promise<void> {
     console.error('Run `gbrain apply-migrations --yes` manually to retry.');
   }
 
+  // v0.28.5 (X1): explicitly apply pending schema migrations.
+  // apply-migrations runs orchestrator migrations and only WARNs about
+  // schema-version drift (apply-migrations.ts:296-302). Without this hook,
+  // `gbrain upgrade` leaves wedged brains wedged — the user has to read
+  // the WARN and run `gbrain init --migrate-only` themselves. We've shipped
+  // 11 wedge incidents asking users to read warnings; close the loop here.
+  // A1's hasPendingMigrations probe in connectEngine is belt-and-suspenders
+  // for any path that bypasses upgrade (autopilot, direct CLI on stale brain).
+  try {
+    const { loadConfig: lcSchema, toEngineConfig: toCfgSchema } = await import('../core/config.ts');
+    const { createEngine } = await import('../core/engine-factory.ts');
+    const cfgSchema = lcSchema();
+    if (cfgSchema) {
+      const engine = await createEngine(toCfgSchema(cfgSchema));
+      try {
+        await engine.connect(toCfgSchema(cfgSchema));
+        await engine.initSchema();
+        console.log('  Schema up to date.');
+      } finally {
+        try { await engine.disconnect(); } catch { /* best-effort */ }
+      }
+    }
+  } catch (e) {
+    // Non-fatal: connection or DDL failure here falls back to the existing
+    // user-facing WARN. apply-migrations.ts:296-302 already surfaces the
+    // hint to run `gbrain init --migrate-only`.
+    const msg = e instanceof Error ? e.message : String(e);
+    console.warn(`\nSchema auto-apply skipped: ${msg}`);
+    console.warn('Run `gbrain init --migrate-only` manually if your brain is wedged.');
+  }
+
   // v0.25.1: agent-readable advisory listing recommended skills the
   // workspace hasn't installed yet. No-op when everything is installed.
   try {