Invisible / "no build tools" projects in workspace not recognized

Additionally to #1672 I found the following problem:

Let's assume my students add new Java project with the Java Projects + wizard in an existing workspace.

If you're in a workspace with the following structure:

workspace_root
workspace_root/project1 --> Maven project

As soon as you add a second "No build tools" Java project like this:

workspace_root/project2 --> "No build tools" Java project

it will not be recognized.

If your structure is like this:

workspace_root
workspace_root/project1 --> "No build tools" Java project
workspace_root/project2 --> "No build tools" Java project

The extension seems like it wants to merge both classpaths and shows errors due to both projects having an App.java

This can easily reproduced by just adding two projects.

I don't know if this problem is related to the nature of invisible projects.

Everything works fine for those no build tools if you open each project in a separate window in VSCode. It's only a problem if you're using workspaces.