v0.8.0

0.7.2 -> 0.8.0
o Added support for Waterman-Eggert style suboptimal alignments
o Fixed bugs with Hughey-style DP traceback
o Fixed bugs with phase model
o Added option for alignment refinement
o Stopped glib error messages from dumping core
o Added --{query,target}chunk{id,total} for splitting up jobs
o Added start of test suite
o Fixed a bug with the shadow designation algorithm
o Added %e[ti] for equivalenced symbol counting
o Turned off --forcegtag by default
o Added query-specific score thresholds
o Added RangeTree-based HSP pairing algorithm
o Made Shadows go state->transition to fix span model problems
o Fixed BSDP to work properly with suboptimal alignments
o Fixed shadow propagation algorithm for derived models.
o Simplified phase model for new shadows

0.7.1 -> 0.7.2
o Moved transition shields to calc
o Fixed a bug caused by shadow designation clashing
o Added shadow to intron model to apply min/max intron limits
o Fixed bugs with 3:3 HSP filtering
o Added general speedups to HSP code
o Bug fix for guessing database type of large files
o Added coding2genome model
o Simplified intron model (fewer states)
o Fixed bugs with shadow assignment ordering
o Fixed compilation when G_GNUC_EXTENSION not defined
o Added option for aggressive HSP filtering
o Removed old terminal_data/secondary_data system for C4_Calc
o Added Alphabet type to replace Sequence_Type and handle masking
o Improved softmasking implementation
o Removed all use of gmodule and renamed Plugin as Codegen,
o Changed bootstrapper for faster linking
o Separated Viterbi code from Optimal module
o Made bootstrapper use C4_COMPILED_MODEL_LIST
o Added Model_Type module
o Fixed sorting of results (on score) with --bestn