I place include (header) and source files in the same directory (folder). I create different folders for different themes. I get frustrated when trying to find header files (while debugging and also for researching). In some shops, there are only two folders: source and includes. These directories tend to grow exponentially. Reusing code becomes a nightmare at best.
IMHO, I believe organizing by theme is better. Each theme folder should build into at least one library. Different projects can easily include the themes by searching or including the folders. The projects only need to include the libraries. Smart build engines can list the theme folders as dependencies. This speeds up the build process.
The theme organization also adds a bit of safety to the project. Accidental damage to files (such as removing the wrong ones or replacing with different versions) is reduced since files are located in different directories. Deletion of files in the "Person" folder will not affect files in the "Shape" folder.
This is just my opinion, Your Mileage May Vary.
