The first 
consideration is what extension to use for the source files. Tradition 
calls for .pl, but conflicts with Perl force the use of 
another extension on systems where extensions have global meaning, such 
as MS-Windows. On such systems .pro is the common 
alternative. On MS-Windows, the alternative extension is stored in the 
registry key
HKEY_CURRENT_USER/Software/SWI/Prolog/fileExtension or
HKEY_LOCAL_MACHINE/Software/SWI/Prolog/fileExtension. All 
versions of SWI-Prolog load files with the extension .pl as 
well as with the registered alternative extension without explicitly 
specifying the extension. For portability reasons we propose the 
following convention:
.pl..pro and use this extension for the files you want 
to load through your file manager. Use
.pl for all other files for maximal portability.
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.
Thanks to Quintus, Prolog adapted an extensible mechanism for searching files using file_search_path/2. This mechanism allows for comfortable and readable specifications.
Suppose you have extensive library packages on graph algorithms, set operations and GUI primitives. These sub-projects are likely candidates for re-use in future projects. A good choice is to create a directory with sub-directories for each of these sub-projects.
Next, there are three options. One is to add the sub-projects to the directory hierarchy of the current project. Another is to use a completely dislocated directory. Third, the sub-project can be added to the SWI-Prolog hierarchy. Using local installation, a typical file_search_path/2 is:
:- prolog_load_context(directory, Dir), asserta(user:file_search_path(myapp, Dir)). user:file_search_path(graph, myapp(graph)). user:file_search_path(ui, myapp(ui)).
When using sub-projects in the SWI-Prolog hierarchy, one should use 
the path alias swi as basis. For a system-wide 
installation, use an absolute path.
Extensive sub-projects with a small well-defined API should define a load file with calls to use_module/1 to import the various library components and export the API.