v2 phase 1: foundation — types, DB layer, logging

Add the v2 data layer: typed interfaces, central DB with migration
runner, per-entity CRUD, and agent-runner session DB operations.

- src/log.ts: concise message-first logging API
- src/types-v2.ts: AgentGroup, MessagingGroup, Session, MessageIn/Out
- src/db/: connection (WAL), migration runner, 001-initial schema,
  CRUD for agent_groups, messaging_groups, sessions, pending_questions
- container/agent-runner/src/db/: session DB connection, messages_in
  reads + status transitions, messages_out writes
- 31 new tests, all 277 tests pass

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/db/migrations/index.ts

@@ -0,0 +1,46 @@
+import type Database from 'better-sqlite3';
+
+import { log } from '../../log.js';
+import { migration001 } from './001-initial.js';
+
+export interface Migration {
+  version: number;
+  name: string;
+  up: (db: Database.Database) => void;
+}
+
+const migrations: Migration[] = [migration001];
+
+export function runMigrations(db: Database.Database): void {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS schema_version (
+      version INTEGER PRIMARY KEY,
+      name    TEXT NOT NULL,
+      applied TEXT NOT NULL
+    );
+  `);
+
+  const currentVersion =
+    (db.prepare('SELECT MAX(version) as v FROM schema_version').get() as { v: number | null })?.v ?? 0;
+
+  const pending = migrations.filter((m) => m.version > currentVersion);
+  if (pending.length === 0) return;
+
+  log.info('Running migrations', {
+    from: currentVersion,
+    to: pending[pending.length - 1].version,
+    count: pending.length,
+  });
+
+  for (const m of pending) {
+    db.transaction(() => {
+      m.up(db);
+      db.prepare('INSERT INTO schema_version (version, name, applied) VALUES (?, ?, ?)').run(
+        m.version,
+        m.name,
+        new Date().toISOString(),
+      );
+    })();
+    log.info('Migration applied', { version: m.version, name: m.name });
+  }
+}