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.