[meta] Package Manager should add validation to try avoid conflicts with non-Composer installed code

Problem/Motivation

Any time Package Manager causes a new package(not in active) that is a Drupal project to be added to the stage directory there is a chance that same Drupal project could be in the active code base but not installed via Composer.

If the stage is then applied then there may be 2 different version of that Drupal project.

Steps to reproduce

Proposed resolution

Possible ways we could detect these problems by checking the staged code base for any new packages of the type drupal-module, drupal-theme, others?

1. #3305568: Create a validator that detects duplicate info.yml files in the stage on apply
2. #3305564: Create a validator to stop newly installed packages from overwriting existing directories on apply

Remaining tasks

Figure out what we can check for