Update mussa build scripts to work with Boost 1.40 and CMake 2.6

For Boost 1.40 the filesystem module now requires linking against
boost system.

For some reason the serialization code in alg/sequence.hpp doesn't
work for the Sequence class.

For CMake I could remove my local FindBoost program as CMake now
ships with FindBoost. (Also I had to change the CMake files to add
the new library.