This cleans up how the CLI parses and handles -E, -S, and -c.
Compilation explicitly acknowledges when it is being used to do C
preprocessing.

-S is properly translated to -fno-emit-bin -femit-asm but Compilation
does not yet handle -femit-asm.

There is not yet a mechanism for skipping the linking step when there is
only a single object file, and so to make this work we have to do a file
copy in link.flush() to copy the file from zig-cache into the output
directory.