Updated defaults to those suggested by @rybern

Also reorganized ordering of some options
Fix indentation
Add study 550 to batch processing
Added more useful filtering functionality

Filtering will now accomodate our immediate use-cases for fresco (can still definitely be expanded upon though). Fixed bug in filtering that was already present before my modifications.

Fixes #24 #25 #26.
Merge pull request #27 from jrrideout/real-data-prep

Filtering, bug fixes, and a few misc. changes
Changed when n_generate is applied from inside the optimization function to when the generator is being initialized
Merge branch 'master' into refactoring

Conflicts:
	fresco/command_line_wrapper.py
Rewrote 'stitching' test outcome function
Removed debugging code
Merge pull request #28 from rybern/refactoring

Refactoring
foobarbaz
Merge pull request #29 from jrrideout/cleanup2

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