fix: check input options presence when updating config from CLI

[Dartui]

This PR fixes issue with config options being overwritten when parsing CLI options.

$input->hasOption method returns true for every input option that is configured (see Console/Commands/Compose@configure), even when input option is not passed from CLI.

Because of that when you are not setting deleteVendorPackages option from CLI, the composer.json extra config is overwritten before doing cleanup action. All input options are optional, so to preserve extra config we should not change values of the config when input option values equals to null.

[BrianHenryIE]

Thank you. I wrote a test for it too 7593385