Update .gitignore file with definitions for autotools files
Fix:  Fix segmentation error when state is declared but not defined.

In finalization of model, a missing state that is declared and not defined cause a segmentation fault.
Added checking of state.  If any state is not defined then error message will warn and exit
Fix:  Mistaken checking of posterior file parameter when not set resulted in warning for every execution

In main, checks for file name when output is -posterior, -gff, -path, -label.    Added if statement to check
to see if any of the command line options were passed.   If so, then get the filename
Bug Fix:  Incorrect/Incomplete parsing of ambiguous track failed to warn

Fixed by checking that ambiguous list was parsed.  If not, then warn and
xit the program.
Added Multivariate Continuous PDF to emissions
Added functions to be initialized at the creation of StateFuncs
Fix StochHMM::sequence::getUndigitzed function to only return sequence

getUndigitized was mistakenly returning sequence as fasta format with header
instead of just a sequence

Removed the inclusion of header
Update version number to 0.30
Fix printing of Posterior table

It was printing complete table to a std::string.  This was leading
to memory doubling when used with very large datasets.
Testing float vs double precision in posterior
Fix missing changes from float_2d to double_2d
Updated Posterior/Forward/Backward to use Traceback table from Viterbi
in order to handle Explicit duration states

Also updated documentation in hmm.h, StochHMMlib.h

Commented out Graphviz printing
Add additional code documentation
Fix concatenation of sequence when calling getFasta sequentially.

When getFasta was called multiple times on a sequence it would concatenate the sequence instead of removing the previous sequence.

Added a check to import functions, if sequences is already defined.  It will now delete and reset the sequence to initial state
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