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Cant you just have it create a project file?
Just create a .bmx file that adds Include statements for every single .bmx file in the project directory and all it's sub directories, as well as any sourcefiles manually added by the user.

That way the user does not have to worry about including them by himself, and you have everything neatly packed into 1 file.

Example code directory

%root%/game.bmx
%root%/graphics/window.bmx
%root%/graphics/texture.bmx
%root%/graphics/mesh.bmx
%root%/graphics/color.bmx
%root%/graphics/rectangle.bmx
%root%/graphics/gl/glwindow.bmx
%root%/graphics/gl/gltexture.bmx
%root%/graphics/gl/glmesh.bmx
%root%/graphics/dx/dxwindow.bmx
%root%/graphics/dx/dxtexture.bmx
%root%/graphics/dx/dxmesh.bmx
%root%/data/database.bmx

then when I create a new project for this in BlIDE, it automaticly generates a .bmx file for all this which is also set as the Build File.

myproject.bmx (build file)

'// optional Strict mode
SuperStrict

'// optional Framework
Framework BRL.GLMax2D

'// Optional Imports
Import BRL.BmpLoader
Import BRL.TGALoader
Import PUB.FreeJoy

'// Included project source files
include "game.bmx"
include "graphics/window.bmx"
include "graphics/texture.bmx"
include "graphics/mesh.bmx"
include "graphics/color.bmx"
include "graphics/rectangle.bmx"
include "graphics/gl/glwindow.bmx"
include "graphics/gl/gltexture.bmx"
include "graphics/gl/glmesh.bmx"
include "graphics/dx/dxwindow.bmx"
include "graphics/dx/dxtexture.bmx"
include "graphics/dx/dxmesh.bmx"
include "data/database.bmx"

you could even make it user-configurable, so he can choose what kind of strict mode is being used. And a user-configurable Framework directive and Imports.

Ideally, you could set a default set of Import/Framework directives that are used in every new project, enless the user explicitly states otherwise.