Persist entries immediately, structured-clone ModelMessage, and add migration for new message format

[mikea]

Motivation

• Message persistence format was changed to store AI SDK ModelMessage JSON directly, which is incompatible with older payloads and requires a DB reset.
• Session state must avoid retaining external object references from callers and AI SDK callbacks, so incoming messages need to be cloned and validated at the boundary.

Description

• Add migration packages/core/migrations/0002_drop_incompatible_sessions.sql that deletes entries and sessions to reset persisted state for the new format.
• Change Messages to structured-clone and validate incoming ModelMessage instances, expose pushAll returning cloned messages, and add slice, replace, and helper cloning logic in packages/core/src/messages.ts.
• Update entry types in packages/core/src/db/entry-types.ts so MessageEntry.data is ModelMessage | { type: "system"; content: string } to support legacy system entries.
• Convert legacy system message payloads during context reconstruction in packages/core/src/session/context.ts so they map to ModelMessage with role: "system".
• Rework AgentSessionDO (packages/core/src/agent-session-do.ts) to remove deferred pendingEntries batching and instead: ensure the sessions row is committed lazily via #ensureSessionCommitted, persist each new entry immediately with appendEntry (renamed import persistEntry), update #leafId/#updatedAt on write, map in-memory cloned messages to persisted entry IDs, and persist compaction entries immediately.
• Update specs in specs/core.md to document immediate persistence and the new message format behaviour.

Testing

• Ran TypeScript build with npm run build (typecheck) and the command completed successfully.
• Ran the automated unit test suite with npm test and all tests passed.

---

Codex Task