Starting work on prefilters for the CQM calculation M/R jobs

This code attempts to look at the measure structure to come up with
a MongoDB query to prefilter records before doing measure calculation.
Currently, this will only work for measures with birthdate criteria
specified in the IPP relative to the measure period. This will require
work in QME to take advantage of the prefilters.
Now building the MongoDB query hash in the measure model
Flip comparitors (they were wrong), removing $and clause (not needed)
Merge pull request #137 from rbclark/duplicate_include

ThingWithCodes is already included by Entry.
Merge pull request #136 from projectcypress/measure_prefilter

Measure prefilter
embedded_in fixes where Mongoid stores Prefilters

Without this statement, Mongoid was putting Prefilters directly in the measures
collection. This breaks a lot of stuff.
Merge pull request #138 from projectcypress/fixing_prefilter_storage

embedded_in fixes where Mongoid stores Prefilters
Updating the README
updating bulk record importer to accept json documents and address issues with loading from directories as well as error handling and testing
Merge branch 'master' of github.com:projectcypress/health-data-standards into json_patient_import
Switching from passing in a File to a Dir

It appears that using JRuby File.new(a_directory) throws a Permission denied
exception. This code works fine with File.new on MRI/YARV.
Merge pull request #139 from projectcypress/json_patient_import

Json patient import
Fixing date calculations in the prefilters

Previously, when calculating the dates for prefilters, we were
calculating a year as just 365 days. This new code uses actual date
functions to account for things like leap years.
Now properly sets the ordinality when importing

Switching the parent class to CDA::ProcedureImporter. This allows us
to use the extract_ordinality method available there. The previous
implementation has its own extract_ordinality method, which assigned
an incorrect structure to ordinality.
Merge pull request #140 from projectcypress/fix_prefilters

Fixing date calculations in the prefilters
Merge pull request #141 from projectcypress/ordinality_fix

Now properly sets the ordinality when importing
fixing cv reporting bug in cat 3 export
updated cv template to except id and value
Merge branch 'cat3_cv_fix'

Rebasing and merging pull request #142
Bumping for v3.4.6