fix: respect removed files from app folder

[Fatme]

PR Checklist

• The PR title follows our guidelines: https://github.com/NativeScript/NativeScript/blob/master/CONTRIBUTING.md#commit-messages.
• There is an issue for the bug/feature this PR is for. To avoid wasting your time, it's best to open a suggestion issue first and wait for approval before working on it.
• You have signed the CLA.
• All existing tests are passing: https://github.com/NativeScript/nativescript-cli/blob/master/CONTRIBUTING.md#contribute-to-the-code-base
• Tests for the changes are included.

What is the current behavior?

File is not deleted from platforms folder if it is deleted from app folder

What is the new behavior?

File is deleted from platforms folder if it is deleted from app folder