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

packages/shared/src/trpc.ts

@@ -1 +1 @@
-export type { AppRouter } from '../../../src/trpc/router.js';
+export type { AppRouter } from '../../../apps/server/trpc/router.js';

packages/shared/src/types.ts

@@ -1,5 +1,5 @@
-export type { Initiative, Phase, Task, Agent, Message, Page, Project, Account, ChangeSet, ChangeSetEntry } from '../../../src/db/schema.js';
-export type { PendingQuestions, QuestionItem } from '../../../src/agent/types.js';
+export type { Initiative, Phase, Task, Agent, Message, Page, Project, Account, ChangeSet, ChangeSetEntry } from '../../../apps/server/db/schema.js';
+export type { PendingQuestions, QuestionItem } from '../../../apps/server/agent/types.js';
 
 export type ExecutionMode = 'yolo' | 'review_per_phase';
 export type PhaseStatus = 'pending' | 'approved' | 'in_progress' | 'completed' | 'blocked' | 'pending_review';