refactor: Restructure monorepo to apps/server/ and apps/web/ layout

Move src/ → apps/server/ and packages/web/ → apps/web/ to adopt
standard monorepo conventions (apps/ for runnable apps, packages/
for reusable libraries). Update all config files, shared package
imports, test fixtures, and documentation to reflect new paths.

Key fixes:
- Update workspace config to ["apps/*", "packages/*"]
- Update tsconfig.json rootDir/include for apps/server/
- Add apps/web/** to vitest exclude list
- Update drizzle.config.ts schema path
- Fix ensure-schema.ts migration path detection (3 levels up in dev,
  2 levels up in dist)
- Fix tests/integration/cli-server.test.ts import paths
- Update packages/shared imports to apps/server/ paths
- Update all docs/ files with new paths

apps/server/db/repositories/message-repository.ts

@@ -0,0 +1,118 @@
+/**
+ * Message Repository Port Interface
+ *
+ * Port for Message aggregate operations.
+ * Implementations (Drizzle, etc.) are adapters.
+ *
+ * Messages persist agent questions for users to query and respond later.
+ * Supports threading via parentMessageId for response linking.
+ */
+
+import type { Message } from '../schema.js';
+
+/**
+ * Message sender/recipient type.
+ */
+export type MessageParticipantType = 'agent' | 'user';
+
+/**
+ * Message type.
+ */
+export type MessageType = 'question' | 'info' | 'error' | 'response';
+
+/**
+ * Message status.
+ */
+export type MessageStatus = 'pending' | 'read' | 'responded';
+
+/**
+ * Data for creating a new message.
+ * Omits system-managed fields (id, createdAt, updatedAt).
+ */
+export interface CreateMessageData {
+  senderType: MessageParticipantType;
+  senderId?: string | null;
+  recipientType: MessageParticipantType;
+  recipientId?: string | null;
+  type?: MessageType;
+  content: string;
+  requiresResponse?: boolean;
+  status?: MessageStatus;
+  parentMessageId?: string | null;
+}
+
+/**
+ * Data for updating a message.
+ * Partial of create data - all fields optional.
+ */
+export type UpdateMessageData = Partial<CreateMessageData>;
+
+/**
+ * Message Repository Port
+ *
+ * Defines operations for the Message aggregate.
+ * Enables message persistence for agent-user communication.
+ */
+export interface MessageRepository {
+  /**
+   * Create a new message.
+   * Generates id and sets timestamps automatically.
+   */
+  create(data: CreateMessageData): Promise<Message>;
+
+  /**
+   * Find a message by its ID.
+   * Returns null if not found.
+   */
+  findById(id: string): Promise<Message | null>;
+
+  /**
+   * Find messages by sender.
+   * @param type - 'agent' or 'user'
+   * @param id - Optional sender ID (agent ID if type='agent', omit for user)
+   * Returns messages ordered by createdAt DESC.
+   */
+  findBySender(type: MessageParticipantType, id?: string): Promise<Message[]>;
+
+  /**
+   * Find messages by recipient.
+   * @param type - 'agent' or 'user'
+   * @param id - Optional recipient ID (agent ID if type='agent', omit for user)
+   * Returns messages ordered by createdAt DESC.
+   */
+  findByRecipient(type: MessageParticipantType, id?: string): Promise<Message[]>;
+
+  /**
+   * Find all pending messages for user.
+   * Returns messages where recipientType='user' and status='pending'.
+   * Ordered by createdAt DESC.
+   */
+  findPendingForUser(): Promise<Message[]>;
+
+  /**
+   * Find all messages requiring a response.
+   * Returns messages where requiresResponse=true and status='pending'.
+   * Ordered by createdAt DESC.
+   */
+  findRequiringResponse(): Promise<Message[]>;
+
+  /**
+   * Find all replies to a message.
+   * @param parentMessageId - The ID of the parent message
+   * Returns messages ordered by createdAt DESC.
+   */
+  findReplies(parentMessageId: string): Promise<Message[]>;
+
+  /**
+   * Update a message.
+   * Throws if message not found.
+   * Updates updatedAt timestamp automatically.
+   */
+  update(id: string, data: UpdateMessageData): Promise<Message>;
+
+  /**
+   * Delete a message.
+   * Throws if message not found.
+   */
+  delete(id: string): Promise<void>;
+}