fix(packaging): dereference restored runtime deps

apps/cli/tests/web-agent-presets.e2e.ts

@@ -366,7 +366,6 @@ describe('the shipped Web composition', () => {
 
     expect(await readFile(path, 'utf8')).toBe(before)
   })
-
 })
 
 describe('a switch survives the session', () => {

scripts/build-exe-for-python-sdk.ts

@@ -296,6 +296,7 @@ class SingleExeBuild {
       const nestedNodeModules = join(source, 'node_modules')
       await cp(source, destination, {
         recursive: true,
+        dereference: true,
         filter: path => path !== nestedNodeModules && !path.startsWith(nestedNodeModules + sep),
       })
       restored.push(dependency)