I add source files by links, not copies. I use "folders" to reflect the actual folders where the source files reside. This works fine with studio 6.2 and earlier versions. It's also the way Visual Studio does it.
However it causes this version of Studio to do crazy things. I have a hard time getting my projects to build. If I don't jump through all the right hoops the builds fail because it can't find the .d and .o files. And I haven't figured out what the right hoops are. I have to use the time honored trial and error method.
I created a simple project with only main.cpp. I didn't put main.cpp directly into the project. I put it into a sibling folder I called Test_folder and created a link to it. This thing builds (glory halleluyah). Then I closed the solution and re-opened it to give you a peek at what studio does. This thing builds too (glory halleluyah all over again). My real projects require a lot of screwing around to get them to build. Before I get them just right to please studio, I get tons of "can't find .d and can't find .o" errors.
I will include a zip folder of this project. If you unzip it and build it, you will see the closed and re-opened version, even though I zipped up the original. You can turn it into the original by sliding main.cpp into the original "Folder" and deleting the extraneous "GccApplication3" folder and the extraneous "Folder". It should build. If you close it and re-open it, the extraneous folders will be back.
I'll make another post illustrating how bizarre things get with a real world example.
and after reopening 
