refactor: consolidate CLI entry points into dedicated cli/ directory

Move `database` and `setup` CLI scripts from their respective feature
directories into a unified `src/cli/` directory. Update `tsup.config.js`
build entries and `package.json` bin paths to reflect the new locations.

tsup.config.js

@@ -16,9 +16,9 @@ export default defineConfig([
       'src/core/api/index.js',
       'src/core/api/nx-route.js',
       'src/core/database/index.js',
-      'src/core/database/cli.js',
       'src/features/setup/index.js',
-      'src/features/setup/cli.js',
+      'src/cli/database.js',
+      'src/cli/setup.js',
       'src/core/email/index.js',
       'src/core/email/templates/index.js',
       'src/core/storage/index.js',