Added the option to align using Hirschberg algorithm, which uses O(n) space and O(nm) time. Major code rewrite - better organization and performance.
[Commented] File used to generate PajeAlign.cc and PajeAlign.h using Lzz C++
[Commented] File used to generate PajeGraph.cc and PajeGraph.h using Lzz C++
Minor changes.
Adapted to PajeAlign changes.