a) (this) is a good practice to make a similar structure in C ++,
One way to find out is to download several open source projects and see their file structure.
In my experience, the build tool used really dictates the file structure. If it is a little painful for you to have many subdirectories with your build tool, then you will not have many subdirectories.
b) if so, what is the best way to configure it?
It depends on the build environment / dev. I personally use vim and tools for Linux files, so I installed it all manually. Someone using Eclipse or Visual Studio may have several wizards to work with.
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