Modernize: replace boost::shared_ptr with std::shared_ptr in template…

[mirams]

…s and reference models

Also add #include to the shared hpp includes template and all reference .hpp files so generated code compiles without boost/shared_ptr.hpp.

Description

Motivation and Context

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Documentation checklist

• I have updated all documentation in the code where necessary.
• I have checked spelling in all (new) comments and documentation.
• I have added a note to RELEASE.md if relevant (new feature, breaking change, or notable bug fix).
• I have updated version & citation.txt & citation.cff version.

Testing

• Testing is done automatically and codecov shows test coverage
• This cannot be tested automatically

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (7878bf3) to head (9f1670c).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff            @@
##            master      #297   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           30        30           
  Lines         1789      1789           
=========================================
  Hits          1789      1789           

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