synchronize class allocation

Removes includes in core/ referencing headers
outside core/.
fix errors in code generation script
cosmetics
remove empty line
codon.h -> codon_api.h
codon_iterator*.h -> codon_iterator*_api.h
disc_distri.h -> disc_distri_api.h
update file_api.h
update fileutils_api.h
md5_encoder.h -> md5_encoder_api.h
md5_fingerprint.h -> md5_fingerprint_api.h
outputfile.h -> output_file{_api.h,.h}
documentation
thread.h -> thread_api.h
tool.h -> tool_api.h
toolbox.h -> toolbox_api.h
version bump
seqiterator*.h -> seq_iterator*.h
seq_iterator*.h -> seq_iterator*_api.h
make sure API header include only API headers