A typical SPI application will have at least three top level directories. The application will be contained in a directory starting with app_, the spi component source is in the module_spi_master|slave directory and the directory module_xcommon contains files required to build the application.
app_[my_app_name]/
module_spi_master|slave/
module_xcommon/
Of course the application may use other modules which can also be directories at this level. Which modules are compiled into the application is controlled by the USED_MODULES define in the application Makefile.