Merge pull request #8 from rybern/refactoring

Did significant refactoring on most sections.
Merge pull request #9 from rybern/refactoring

Refactoring
Update example command in README.md
Rename command_line_script.py to fresco.py
Update README.md to reference new script name
Fix feature vector output

Fixes #10.
Add --output_dir option

Removed --prediction_testing_output and --feature_vector_output. Fixes #5.
Merge pull request #11 from jrrideout/misc-fixes

Misc. changes
Added a 'stitch_avg_outcome' function, which builds an average outcome from a list of masks used in cross validation. Added this function for writing the feature scores of test results.