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

docs/cli-config.md

@@ -1,10 +1,10 @@
 # CLI & Configuration
 
-`src/cli/` — CLI commands, `src/config/` — workspace configuration, `src/bin/` — entry point.
+`apps/server/cli/` — CLI commands, `apps/server/config/` — workspace configuration, `apps/server/bin/` — entry point.
 
 ## Entry Point
 
-`src/bin/cw.ts` — hashbang entry that imports and runs the CLI.
+`apps/server/bin/cw.ts` — hashbang entry that imports and runs the CLI.
 
 ## CLI Framework
 
@@ -136,7 +136,7 @@ This includes all repositories, managers, and the credential manager. The server
 
 ## Workspace Configuration
 
-`src/config/` module:
+`apps/server/config/` module:
 
 ### .cwrc File
 JSON file at workspace root that marks a `cw` workspace: