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

tests/integration/cli-server.test.ts

@@ -6,12 +6,12 @@
  */
 
 import { describe, it, expect, beforeAll, afterAll } from 'vitest';
-import { CoordinationServer } from '../../src/server/index.js';
-import { ProcessManager, ProcessRegistry } from '../../src/process/index.js';
-import { LogManager } from '../../src/logging/index.js';
-import { createEventBus } from '../../src/events/index.js';
-import { createTrpcClient } from '../../src/cli/trpc-client.js';
-import type { TrpcClient } from '../../src/cli/trpc-client.js';
+import { CoordinationServer } from '../../apps/server/server/index.js';
+import { ProcessManager, ProcessRegistry } from '../../apps/server/process/index.js';
+import { LogManager } from '../../apps/server/logging/index.js';
+import { createEventBus } from '../../apps/server/events/index.js';
+import { createTrpcClient } from '../../apps/server/cli/trpc-client.js';
+import type { TrpcClient } from '../../apps/server/cli/trpc-client.js';
 
 describe('CLI-Server Integration', () => {
   let server: CoordinationServer;