I've created the following directory structure:-
Header Files
Resource Files
Source Files
At times (and I haven't figured out the exact timing),
but after closing and reopening the .dev file, the
following folder structure appears, inclusive of all
files (duplicate).
Header Files
Resource Files
Source Files
Header Files
Resource Files
Source Files
I also noticed when I open the .dev file in wordpad,
that "Resource Files" isn't inside "" and 1 area simply
referred to Resource.
The solution 'might' be as simple as ensuring the
program adds "" around all directory names when
creating .dev files (especially folder names with
spaces). By directly modifying the .dev file with
these, it fixed the problem.