This may be a silly question,
gcc-help is for silly questions...
But why is the /gcc4.1/include/ directory empty?
Why not?
I expected to see that directory filled with *.h files and a sys/ directory.
Ok, but why?
It's not there?
Right.
Which files are included when I compile my stuff?
gcc -E will tell you this, as will -H, as documented in the manual.
try
ls /usr/include
maybe there are some headers in that directory.