Sushi upgrade 22

[coxstuart]

ISSUE #35 - UPGRADE IG TO SUSH 2.2

- NPM vulnerabilities reduced:  31 to 19
- High vulnerabilities reduced:  8 to 6

CHANGE SUMMARY

- Renamed config.yaml to sushi.config.yaml
- Updated sushi-config.yaml content and comments to match new sushi template
    - Changed release label to draft (see FHIR release label guidance)
    - Added jurisdiction = US (default from sushi init)
    - Added url for publisher (linked to Alvearie site)
    - Set apply-contact false to prevent contacts from being added to resource samples in the IG
    - Remove test-history path and history section, not working as intended
- Changed folder structures for Sushi 2.2
    - Moved fsh files to data/input/fsh folder (Sushi 2.2 style)
    - Moved custom template files to work with Sushi 2.2
        - Moved alvearie-template folder to data/
        - Moved ig.ini file to data/
        - Point ig.ini to new alvearie-template path
        - Moved include folder to data/input
        - Removed ig-data folder (obsolete)
    - Updates to get build working with Sushi 2.2
        - Point ig.ini to new alvea
        - Added data/fsg-generated file to gitignore
    - Removed extra package.json in data folder (obsolete)
    - Removed docs folder (obsolete)
- Fixed profiles that were breaking Sushi 2.2 compiler
    - Removed duplicate extensions
        - InsightValue
        - SourceFieldID
    - Fixed fsh lines with spaces on front before *
        - CDM_Patient_WithDataQaulityInsights_Instance.fsh
        - CDM_Condition_WithNLPInsights_Instance.fsh
        - CDM_Coverage.fsh
    - Fixed broken valueset references
    - Episode extensions modified to use CURRENCY#USD
    - Fixed duplicate inline examples 
        - Patient1
        - IBM
        - Genesys (now CommunicationVendor1)
        - AttributedPractitioner2
    - Fixed missing indexes in PatientMatch example
- Npm script and CI build github actions modifications
    - Updated build scripts to work with new folder structures
    - Changed from copy to rsync (works better for mac users)
    - Removed ping from _updatePublisher.sh to prevent CI Build failures
    - Added version info to CI Build github actions output
- Corrected template styles (footer display colors)

ISSUE #64 - CLEAN UP IG QA ERRORS AND WARNINGS

- QA Errors reduced: 127 to 29
- QA Warnings reduced: 126 to 10
- QA Info reduced: 406 to 8
- Broken links reduced: 3657 to 2

CHANGE SUMMARY

- Added ignoreWarrnings.txt file to suppress known warnings that can't be corrected
- Fixed incorrect profile on ConditionInstanceWithNLPInsights
- Corrected code descriptions on ConditionInstanceWithNLPInsights to fix terminology warnings
- Added caseSensitive = true to all code systems
- EngagementCommunicationRequestReason code system changes:
    - Fixed typo on url 
    - Fixed long descriptions on two codes
- Changed QualityMeasureExample useContext.code to #focus
- ObservationExample changes:
    - Corrected Typo on #vitalsigns
    - Corrected mm[Hg] codes
    - Use aliased code systems
- CDMPatientDeceasedExample changes:
    - Fix url for local-marital-status coding system
- Correcting code system aliases:
   - http://terminology.hl7.org/CodeSystem/definition-topic

• Added missing description to CDMPractionerRole
• Use oid code systems where needed to prevent terminology QA errors
  • Added OID aliases
  • Use OIDs for appointment serviceCategory and serviceType
  • Use OIDs for encounter serviceType
  • Use OIDs for coverage emplyeeJobTitle
  • Use OIDs for organization SIC on type.coding
• Fixed some slicing errors
  • Added identifier slices for identifier type codes used in examples
  • Added CareGap slice to Measure / MeasureReport
• Fixed patientImportance cardinality error
• Fixed broken links and references
  • Added some examples for references used in examples
  • Using inline examples as contained references to prevent QA broken link errors
  • Fixed canonical measure reference errors
• Fixed valueset / coding system issues, use system urls and not aliases
• Added measureScore to measure reports (required for proportion measures)
• Removed WorkAddress profile (obsolete)
• Added multiple data types to insight-value extension (had none)
• Fixed library example errors
  • Using compliant names
  • Added code systems required for data requirements section
  • Fixed library canonical and reference errors

[dmangum2]

I think I've looked at all of the changes. 2 general areas to talk about:

1. using url vs. alias for code system
2. claim sequence invariant issue - still working on logic

Thanks for working on all of this!

[dmangum2]

I think I've looked at all of the changes. 2 general areas to talk about:

1. using url vs.  alias for code system

2. claim sequence invariant issue - still working on logic

Thanks for working on all of this!

Followup 1/21/2022-

1. The alias was generating warnings so changed to use URL. Need to remember to check QA report after any new changes.
2. Removing the invariant until it can be resolved.

[dmangum2]

Requested changes look good.

[kimkenna]

Thanks for addressing the comments I had to you in slack. I approve of this PR! Great work!