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/agent/lifecycle/cleanup-strategy.ts

@@ -0,0 +1,108 @@
+/**
+ * CleanupStrategy — Centralized cleanup logic based on debug mode and agent state.
+ *
+ * Determines when and how to clean up agent workdirs and resources.
+ * Supports archive mode for debugging vs. immediate cleanup for production.
+ */
+
+import { createModuleLogger } from '../../logger/index.js';
+import type { CleanupManager } from '../cleanup-manager.js';
+
+const log = createModuleLogger('cleanup-strategy');
+
+export type CleanupAction = 'remove' | 'archive' | 'preserve';
+
+export interface AgentInfo {
+  id: string;
+  name: string;
+  status: string;
+  initiativeId?: string | null;
+  worktreeId: string;
+}
+
+export interface CleanupStrategy {
+  shouldCleanup(agent: AgentInfo, isDebugMode: boolean): Promise<CleanupAction>;
+  executeCleanup(agent: AgentInfo, action: CleanupAction): Promise<void>;
+}
+
+export class DefaultCleanupStrategy implements CleanupStrategy {
+  constructor(private cleanupManager: CleanupManager) {}
+
+  /**
+   * Determine what cleanup action should be taken for an agent.
+   * Considers agent status and debug mode setting.
+   */
+  async shouldCleanup(agent: AgentInfo, isDebugMode: boolean): Promise<CleanupAction> {
+    log.debug({
+      agentId: agent.id,
+      name: agent.name,
+      status: agent.status,
+      isDebugMode
+    }, 'evaluating cleanup action for agent');
+
+    // Never cleanup agents waiting for user input
+    if (agent.status === 'waiting_for_input') {
+      log.debug({ agentId: agent.id, status: agent.status }, 'preserving agent waiting for input');
+      return 'preserve';
+    }
+
+    // Never cleanup running agents
+    if (agent.status === 'running') {
+      log.debug({ agentId: agent.id, status: agent.status }, 'preserving running agent');
+      return 'preserve';
+    }
+
+    // For completed/idle/crashed agents, decide based on debug mode
+    if (agent.status === 'idle' || agent.status === 'completed' || agent.status === 'crashed') {
+      if (isDebugMode) {
+        log.debug({ agentId: agent.id, status: agent.status }, 'archiving agent in debug mode');
+        return 'archive';
+      } else {
+        log.debug({ agentId: agent.id, status: agent.status }, 'removing agent in production mode');
+        return 'remove';
+      }
+    }
+
+    // For stopped agents, clean up immediately regardless of debug mode
+    if (agent.status === 'stopped') {
+      log.debug({ agentId: agent.id, status: agent.status }, 'removing stopped agent');
+      return 'remove';
+    }
+
+    // Default to preserve for any unrecognized status
+    log.debug({ agentId: agent.id, status: agent.status }, 'preserving agent with unrecognized status');
+    return 'preserve';
+  }
+
+  /**
+   * Execute the determined cleanup action.
+   */
+  async executeCleanup(agent: AgentInfo, action: CleanupAction): Promise<void> {
+    log.debug({
+      agentId: agent.id,
+      name: agent.name,
+      action
+    }, 'executing cleanup action');
+
+    switch (action) {
+      case 'remove':
+        await this.cleanupManager.removeAgentWorktrees(agent.name, agent.initiativeId ?? null);
+        await this.cleanupManager.removeAgentBranches(agent.name, agent.initiativeId ?? null);
+        await this.cleanupManager.removeAgentLogs(agent.id);
+        log.info({ agentId: agent.id, name: agent.name }, 'agent workdir and resources removed');
+        break;
+
+      case 'archive':
+        await this.cleanupManager.archiveForDebug(agent.worktreeId, agent.id);
+        log.info({ agentId: agent.id, name: agent.name }, 'agent workdir archived for debugging');
+        break;
+
+      case 'preserve':
+        log.debug({ agentId: agent.id, name: agent.name }, 'agent workdir preserved');
+        break;
+
+      default:
+        log.warn({ agentId: agent.id, action }, 'unknown cleanup action, preserving by default');
+    }
+  }
+}