update viterbi file

- update variables to reflect usage.
update viterbi file

- update variables to reflect usage.
update generator code

- add help text
- add count input parameter
- refactor option 'all' to 'verbose'
  For clarity, option 'all' is changed to 'verbose'
update generator

- move main execution to top of file.
update viterbi

- move main execution to top of file
- separate training data processing to separate function
update help messages

- update generator help message
- update viterbi help message
clean up debug messages

- clean up debug messages
clean up viterbi processor
add logarithm testing
update log test
refactor markov data to markov data example

- rename markov.data to markov.data.example
rename generator to hmm
refactor generator.pl to generator/markov_chain.pl
move viterbi.pl to solver/viterbi.pl
stop tracking test file.
update to use log probabilities
Add initial vagrant file
update README file
fix initialization bug

- fix initialization bug
Merge pull request #3 from novastorm/develop

update project files