Large projects are generally composed of sub-projects, each using its own directory or directory structure. If nobody else will ever touch your files and you use only one computer, there is little to worry about, but this is rarely the case with a large project.
To improve portability, SWI-Prolog uses the POSIX notation for 
filenames, which uses the forward slash (//\\\
Portable code should use prolog_to_os_filename/2 to convert computed paths into system paths when constructing commands for shell/1 and friends.