diff --git a/src/core/migrate.ts b/src/core/migrate.ts
index 7b95a5767..1e42a958f 100644
--- a/src/core/migrate.ts
+++ b/src/core/migrate.ts
@@ -135,7 +135,10 @@ export const MIGRATIONS: Migration[] = [
           }
         }
       }
-      if (renamed > 0) console.log(`  Renamed ${renamed} slugs`);
+      // Migration progress goes to stderr — stdout must stay clean for
+      // callers parsing JSON (e.g. `gbrain doctor --json | jq`); migrations
+      // can run lazily inside ANY command's first DB connect.
+      if (renamed > 0) process.stderr.write(`  Renamed ${renamed} slugs\n`);
     },
   },
   {
@@ -5572,7 +5575,10 @@ export const MIGRATIONS: Migration[] = [
       await engine.executeRaw(recreateChunksFn);
 
       if (lang === 'english') {
-        console.log(`  v123: trigger functions recreated with language='english' (default — no backfill needed)`);
+        // stderr, NOT stdout: migrations run lazily inside any command's
+        // first DB connect — a console.log here polluted `doctor --json`
+        // stdout and broke jq consumers (heavy-tests fm_wallclock).
+        process.stderr.write(`  v123: trigger functions recreated with language='english' (default — no backfill needed)\n`);
         return;
       }
 
@@ -5593,7 +5599,7 @@ export const MIGRATIONS: Migration[] = [
         WHERE search_vector IS NOT NULL;
       `);
 
-      console.log(`  v123: trigger functions recreated with language='${lang}' + backfilled existing rows`);
+      process.stderr.write(`  v123: trigger functions recreated with language='${lang}' + backfilled existing rows\n`);
     },
   },
 ];
diff --git a/test/migrate-stdout-clean.test.ts b/test/migrate-stdout-clean.test.ts
new file mode 100644
index 000000000..f33e194b0
--- /dev/null
+++ b/test/migrate-stdout-clean.test.ts
@@ -0,0 +1,68 @@
+/**
+ * Migrations must never write to stdout — regression for the heavy-tests
+ * fm_wallclock failure (run 29731426470).
+ *
+ * Migrations run lazily inside ANY command's first DB connect (initSchema →
+ * runMigrations), including JSON-emitting commands like `gbrain doctor --json`.
+ * The v123 FTS migration (#2941) printed its completion notice via
+ * `console.log`, which landed as the first line of `doctor --json` stdout and
+ * broke every jq consumer ("Invalid numeric literal at line 1, column 7").
+ * runMigrations' own contract (see the comment above its progress writes)
+ * routes ALL migration noise to stderr.
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { runMigrations } from '../src/core/migrate.ts';
+
+describe('migration output stays off stdout', () => {
+  let engine: PGLiteEngine;
+
+  beforeAll(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+  });
+
+  afterAll(async () => {
+    await engine.disconnect();
+  });
+
+  test('re-running pending migrations (v122 → latest) writes nothing to stdout', async () => {
+    // Rewind the version stamp so the v123 handler actually re-executes —
+    // the exact state a CI Postgres/older brain is in when doctor connects.
+    await engine.setConfig('version', '122');
+
+    const stdoutWrites: string[] = [];
+    const origWrite = process.stdout.write.bind(process.stdout);
+    const origLog = console.log;
+    process.stdout.write = ((chunk: unknown, ...rest: unknown[]) => {
+      stdoutWrites.push(String(chunk));
+      return (origWrite as (...a: unknown[]) => boolean)(chunk, ...rest);
+    }) as typeof process.stdout.write;
+    console.log = (...args: unknown[]) => { stdoutWrites.push(args.map(String).join(' ')); };
+
+    try {
+      const res = await runMigrations(engine);
+      // Load-bearing: the migration must have actually run for the stdout
+      // assertion to prove anything.
+      expect(res.applied).toBeGreaterThanOrEqual(1);
+    } finally {
+      process.stdout.write = origWrite;
+      console.log = origLog;
+    }
+
+    expect(stdoutWrites).toEqual([]);
+  }, 60000);
+
+  test('migrate.ts contains no console.log (all migration noise goes to stderr)', () => {
+    const src = readFileSync(join(import.meta.dir, '../src/core/migrate.ts'), 'utf8');
+    const offenders = src
+      .split('\n')
+      .map((line, i) => ({ line, n: i + 1 }))
+      .filter(({ line }) => line.includes('console.log('));
+    expect(offenders).toEqual([]);
+  });
+});
diff --git a/tests/heavy/frontmatter_scan_wallclock.sh b/tests/heavy/frontmatter_scan_wallclock.sh
index b3b952069..162e4d129 100755
--- a/tests/heavy/frontmatter_scan_wallclock.sh
+++ b/tests/heavy/frontmatter_scan_wallclock.sh
@@ -92,11 +92,22 @@ timeout 120s bun run src/cli.ts init --pglite --yes --no-embedding >> "$LOG" 2>&
 
 # Register the brain dir as a source. Use raw SQL since `gbrain sources add`
 # might not exist in this version-window; the schema is what doctor reads.
+# NOTE: must be `bun -e`, not `bun run -e` — `bun run` treats -e as an
+# unknown script name and dumps its usage/script listing with exit 0, so the
+# INSERT silently never ran and doctor scanned zero sources (vacuous pass).
+# Resolve the engine the same way the CLI does (config + env), so the source
+# lands in the DB doctor actually reads (Postgres when CI sets DATABASE_URL,
+# the PGLite brain otherwise) — a hardcoded `connect({})` is in-memory and
+# the INSERT would vanish.
 echo "[fm_wallclock] register source..." | tee -a "$LOG"
-bun run -e "
-import { PGLiteEngine } from './src/core/pglite-engine.ts';
-const e = new PGLiteEngine();
-await e.connect({});
+bun -e "
+import { loadConfig, toEngineConfig } from './src/core/config.ts';
+import { createEngine } from './src/core/engine-factory.ts';
+const cfg = loadConfig();
+if (!cfg) throw new Error('no gbrain config — init failed?');
+const engineConfig = toEngineConfig(cfg);
+const e = await createEngine(engineConfig);
+await e.connect(engineConfig);
 await e.initSchema();
 await e.executeRaw(
   \"INSERT INTO sources (id, name, local_path) VALUES ('fm-wallclock', 'Frontmatter wallclock test', \\\$1)\",