Reorganization of the comparison code.

Moved comparison function implementation to Comparison.cpp and added
simple_compare and aa_compare.

TOD0:
Implement comparison mode switching and a simple way to get the
right slice for different comparisons (e.g. codons or aa comparison).
Added clear_line to utils.cpp.

clear_line is used to clear the command area after a command has
executed or been canceled. It is a cleaner way to do it than having
a loop in handle_special_command.

Also added a short to do list for handle_special_command().