Apologies for the delayed response. The angular-cli.json is indeed created but is hidden and is now .angular-cli.json. Click on ‘View Menu’ in the Project Explorer view (little down arrow in the upper right corner of the view ) and select ‘Customize View’. Uncheck the .*resources filter and you will now be able to see the .angular-cli.json in the project structure.
Sorry for inconvenience caused. Please let us know how it works for you.