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/agent-repository.ts

@@ -0,0 +1,119 @@
+/**
+ * Agent Repository Port Interface
+ *
+ * Port for Agent aggregate operations.
+ * Implementations (Drizzle, etc.) are adapters.
+ */
+
+import type { Agent } from '../schema.js';
+import type { AgentMode } from '../../agent/types.js';
+
+/**
+ * Agent status values.
+ */
+export type AgentStatus = 'idle' | 'running' | 'waiting_for_input' | 'stopped' | 'crashed';
+
+/**
+ * Data for creating a new agent.
+ * Omits system-managed fields and makes optional fields explicit.
+ */
+export interface CreateAgentData {
+  name: string;
+  worktreeId: string;
+  taskId?: string | null;
+  initiativeId?: string | null;
+  sessionId?: string | null;
+  status?: AgentStatus;
+  mode?: AgentMode; // Defaults to 'execute' if not provided
+  provider?: string; // Defaults to 'claude' if not provided
+  accountId?: string | null;
+}
+
+/**
+ * Data for updating an existing agent.
+ * All fields optional. System-managed fields (id, createdAt, updatedAt) are excluded.
+ */
+export interface UpdateAgentData {
+  name?: string;
+  worktreeId?: string;
+  taskId?: string | null;
+  initiativeId?: string | null;
+  sessionId?: string | null;
+  status?: AgentStatus;
+  mode?: AgentMode;
+  provider?: string;
+  accountId?: string | null;
+  pid?: number | null;
+  exitCode?: number | null;
+  outputFilePath?: string | null;
+  result?: string | null;
+  pendingQuestions?: string | null;
+  userDismissedAt?: Date | null;
+  updatedAt?: Date;
+}
+
+/**
+ * Agent Repository Port
+ *
+ * Defines operations for the Agent aggregate.
+ * Enables agent state persistence for session resumption and listing.
+ */
+export interface AgentRepository {
+  /**
+   * Create a new agent.
+   * Generates id and sets timestamps automatically.
+   * Name must be unique.
+   */
+  create(agent: CreateAgentData): Promise<Agent>;
+
+  /**
+   * Find an agent by its ID.
+   * Returns null if not found.
+   */
+  findById(id: string): Promise<Agent | null>;
+
+  /**
+   * Find an agent by its human-readable name.
+   * Returns null if not found.
+   */
+  findByName(name: string): Promise<Agent | null>;
+
+  /**
+   * Find an agent by its associated task.
+   * Returns null if no agent is assigned to that task.
+   */
+  findByTaskId(taskId: string): Promise<Agent | null>;
+
+  /**
+   * Find an agent by its Claude CLI session ID.
+   * Used for session resumption.
+   * Returns null if not found.
+   */
+  findBySessionId(sessionId: string): Promise<Agent | null>;
+
+  /**
+   * Find all agents.
+   * Returns empty array if none exist.
+   */
+  findAll(): Promise<Agent[]>;
+
+  /**
+   * Find agents by status.
+   * Returns empty array if no agents have that status.
+   */
+  findByStatus(status: AgentStatus): Promise<Agent[]>;
+
+  /**
+   * Update an agent with partial data.
+   * Only provided fields are updated, others remain unchanged.
+   * Throws if agent not found.
+   * Updates updatedAt timestamp automatically.
+   */
+  update(id: string, data: UpdateAgentData): Promise<Agent>;
+
+  /**
+   * Delete an agent.
+   * Throws if agent not found.
+   */
+  delete(id: string): Promise<void>;
+}