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In the project window you can organize the project files into some "virtual" folders (Source Files, Include Files, ...)
If you right-click on the project name, you can add a folder with the item "Add Folder...".
If you right-click on one of these folders, you can add one or more files files.
But it's impossible to create a subfolder of one of these folders.
Every large project has a lot of files (sources, ini-files, images, icons, ...), so I think it's quite common having them saved into different "real" folders and subfolders. If you don't explicitly add these files to the project, you can add them to the distribution kit browsing your hard disk "real" folders, but in this situation the absolute path of the files is used. And if you move all your project from a PC to another one you won't be able to recreate the distribution kit without errors if you don't save the whole project to the same folder you use in the first PC.
And this is a really big problem.
For files explicitly added to the project, instead, the relative path is used, and this is OK, so the best situation is to add all the files in the project window.
So it's necessary create a full structure of virtual folders and subfolders.
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