Hi,

Good question. No it's not a bug. 

When building Arduino projects the real build folder is located under "user/temp data". Build clean correctly clears the compiler cache from the temp location.

After an Arduino build, if atmel studio is being used, the output files are copied from the build folder to the current configurations "release/debug" debug folder. The reason for the output file copy is simply to make it easier for people to use native Atmel Studio tools (which expect to find the output files in a different location to the arduino build folder).

You can see the "real build folder" by switching on "tools/options/visual micro/compiler/show build folder", then click build and the path will be displayed in the output window.

You are right but because Visual Micro did not create the folder it might have files in it that Visual Micro didn't create. It's difficult to know if the files in the config/output folders were put there by visual micro or not.

So it just seemed safer and no harm but I am not sure what is the right thing to do so do nothing