coding style
add toolbox class to core/
make chseqids tool a Tool object
make gt_clean() a GtTool object
make gt_merge() a GtTool object
make gt_mmapandread() a GtTool object
make gt_seqstat() a GtTool object
extract method; make sure md5_seqid is used correctly
fix bug in and simplify gt_region_mapping_get_sequence_length()
make offset optional; bug fix
bug fix (regression)
allow to compile with assert=no
improve documentation
coding style
initialize variable

this fixes an error on Mac OS X 10.8.2
splint-clean new tool