how can i keep the directory and subdirectory's relationship

my source code has many directories,when i make the setup program,i want to keep the directories' relationship
second,the File attribute i just specfy a file,other files are called by this file,but other files are not specified to the File attribute,are the other files involved in the setup program?
how can work out these problem
thanks a lot

To include a folder with it's contents, use File /r.