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.
updating bulk record importer to accept json documents and address issues with loading from directories as well as error handling and testing
Updating the README
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.
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.
fixing cv reporting bug in cat 3 export
updated cv template to except id and value
Bumping for v3.4.6
Correctly handle "Concurrent" with Measurement Period Start or End

When the HQMF parser sees references to Measurement Period Start and
Measurement Period End these are converted to Start of Measurement
Period and End of Measurement Period; this commit adds support for the
"Concurrent" operators during this conversion, ie SCW MPE -> SCWE MP
ThingWithCodes is already included by Entry. Including it again causes a warning with mongoid4 because the field codes is being redeclared. Removing the duplicate include stops the warning and does not seem to cause any additional issues.