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/prompts/index.ts

@@ -0,0 +1,14 @@
+/**
+ * Agent Prompts — per-mode prompt builders and shared instructions.
+ *
+ * Each agent type lives in its own file. Shared instructions (signal format,
+ * input files, ID generation) are in shared.ts.
+ */
+
+export { SIGNAL_FORMAT, INPUT_FILES, ID_GENERATION, CONTEXT_MANAGEMENT, DEVIATION_RULES, GIT_WORKFLOW, TEST_INTEGRITY, SESSION_STARTUP, PROGRESS_TRACKING, buildInterAgentCommunication } from './shared.js';
+export { buildExecutePrompt } from './execute.js';
+export { buildDiscussPrompt } from './discuss.js';
+export { buildPlanPrompt } from './plan.js';
+export { buildDetailPrompt } from './detail.js';
+export { buildRefinePrompt } from './refine.js';
+export { buildWorkspaceLayout } from './workspace.js';