Bug Fix:  Add missing files to makefile.am, missing #defines and includes

1. Added bitwise_ops.cpp and dynamic_bitset.cpp to makefile.am
2. Added missing #define statements for SIZE_MAX and CHAR_BIT
3. Added missing header inclusion for stdlib.h in bitwise_ops
and dynamic_bitset
4. Changed use of uint16_t to int16_t for Transition Traceback
function recently added for calling User-defined functions
Fix sparsearray operator[] const

Was copied from nonconst version which changed the sparsearray
Deleted lines of code which changed sparsearray
Also added const to methods for dynamic_bitset::size,
dynamic_bitset::count,and dynamic_bitset::count_before methods
Update to v0.29