Added a -root option to specify the "root" of the compilation
It is mandatory since cmos and cmis are written in a subdirectory that
corresponds to their namespace. However, if the user wants the source to be in
the same folder of the namespace, the compiler must write (and read) from the
root. For example, let assume the following file : m.ml, which is in the
namespace N. Our program/library sources are organized the following:
./main.ml ...
  n/... m.ml

If "m.ml" is compiled without root, it will create a subfolder "n" in "n". If
root is specified as "..", the compilation result will be in the correct "n".