All of Quake's data access is through a hierarchical file system, the contents of the file system can be transparently merged from several sources.

The "base directory" is the path to the directory holding the quake.exe and all game directories. The sys_* files pass this to host_init in quakeparms_t->basedir. This can be overridden with the "-basedir" command line parm to allow code debugging in a different directory. The base directory is only used during filesystem initialization.

The "game directory" is the first tree on the search path and directory that all generated files (savegames, screenshots, demos, config files) will be saved to. This can be overridden with the "-game" command line parameter. If multiple "-game <gamedir>" args are passed the last one is the "primary" and files will be saved there, the rest are read-only.