Corrected many bugs

decoder/src/Decoder.cpp

decoder/src/macaon_decode.cpp

maca_common/include/LimitedArray.hpp

maca_common/include/ProgramParameters.hpp

maca_common/include/util.hpp

maca_common/src/ProgramParameters.cpp

maca_common/src/util.cpp

trainer/src/Trainer.cpp

trainer/src/macaon_train.cpp

transition_machine/include/Config.hpp

transition_machine/src/Config.cpp