Cleaned up interface

First step for refactoring:
 * Add namespace to classes
 * Move types into classes
 * Remove `using namespace std' and add explicit namespace usages to types
 * `for'-loop simplification (c++0x-features)
 * Change names of classes and get rid of `C'-prefix
 * Add functions for adding atomic values (not lists, not key/value-pairs)
 * Add TODOs
 * Add comments on code to refactor
 * General code-cleanup

More to come.
Removed the is_atom field setting for now