You used to be able to - I did it once, but it was a hack and slash job and had to be redone with updates.
In the end I gave it up and switched to having a template project in the workspace that I copy instead. Being a user file, it's not affected by updates.
The template project uses include files in a common location so there is less to copy.
// Source Includes and Initialisation
// Core Module must be First,
#include "../~inc/core.agc"
Core_Init()
// Display Module Second
#include "../~inc/display.agc"
Display_Init( DISPLAY_MODE_NATIVE )
// Optional Vector2D Module ( with basic timer based physics )
#constant VECTOR2D_MAXOBJECTS 100
#include "../~inc/vector2D.agc"
Vector2D_Init( VECTOR2D_MAXOBJECTS )
// App Specific Initialisation
// Loop Code
do
Core_LoopStart()
Display_LoopStart()
Vector2D_LoopStart( Core.lastFrameTime )
Display_LoopEnd()
loop
end