v0.7.0

0.6.7 -> 0.7.0
o Imported various fasta format file processing utilities
o Added --intronpenalty
o Added shadow transitions to C4
o Added protein2genomic model
o Refactored DP core by addition of Optimal_Data
and replacement of various hacks with proper 4D row data.
o Refactored codegen to use a single viterbi function per plugin.
o Modified Optimal_PatternMatrix system to reduce length
of generated code and decrease compile time.
o Fixed bootstrapper to use C4_CC and C4_CFLAGS
o Changed WordHood generation alglorithm to utilise
separate input and output alphabets.
o Changed FSM implementation to allow more control when combining
words which are redundant or subsequences of each other.
o Imported ipcress and reimplemented most of it to handle
mismatches, mixed length and redundant primers etc.
o Changed ./configure --enable-gprof to work
with profiling version of libc6
o Changed argument handling code to parse lists from command line
o Added CompoundFile module
o Made exonerate work with multiple sequence query and target files
o Added more info to man page for exonerate
o Wrote man page for ipcress
o Added more sequence checking when using assertions.
o Fixed bug with display of equivalenced Ns
o Fixed attribute fields and off-by-one coordinate bugs in GFF.
o Added --bestn option for best-in-genome type searches etc.
o Changed --scanquery to --forcescan and made default selection
automatic based on sizes of input files.
o Fixed to parse non-standard DATE format on OS-X.
o Simplified HPair code by addition of SAR module.
o Simplified HSPset code by using HSP horizon
o Simplified DNA2Protein model