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

tsconfig.json

@@ -4,7 +4,7 @@
     "module": "NodeNext",
     "moduleResolution": "NodeNext",
     "outDir": "./dist",
-    "rootDir": "./src",
+    "rootDir": "./apps/server",
     "strict": true,
     "esModuleInterop": true,
     "declaration": true,
@@ -12,6 +12,6 @@
     "forceConsistentCasingInFileNames": true,
     "resolveJsonModule": true
   },
-  "include": ["src/**/*"],
+  "include": ["apps/server/**/*"],
   "exclude": ["node_modules", "dist"]
 }