Project files will contain a <paths> section, which will contain one <projectpath> element, along with zero or more <path> elements. The <projectpath> will be an absolute path to the .pjxml file on the development machine; all <path> entries will be relative to this base project path.
All paths will be stored using normal forward slashes; on Windows these will be converted internally to backslashes as needed. Furthermore, since Windows does not support UNC pathing very well, an option available to Windows-only sites will be to add the drive attribute to the path tag. This will make that <path> entry into an absolute path for the given drive letter. Example:
<path drive="E">/some/directory/and/file.txt</path>
will resolve to:
E:\some\directory\and\file.txt