Here is a short list of useful commands that you can use from your shell (in addition to running emacs and compiling and running your program).
Every directory provides you access to two directories: . (the current directory) and .. (the parent directopry).
Note that ls -F, ls -l, ls -al, ls -alF etc and even simply ls also work. Try out and find the differences. In fact, the ls takes a lot of other options.
cp file1.c file2.c cp file2.c mydir/file3.c
mv file1.c file2.c mv file2.c mydir/ cd mydir/ mv file2.c ../file1.c cd ../
Note: A deleted (by rm) or overwritten (by mv) file is lost for ever. In no way you can get it back. Be very, very careful, before running these commands.