Deprecate the whole modelCompiler API

[alexander-yevsyukov]

This PR deprecates the whole API in favour of the recently introduced root proejct and settings extensions in ToolBase.

Unfortunately, config was updated before the decision to create new API in ToolBase was made. That's why the number of changed files is that big.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.11%. Comparing base (84155cb) to head (1ba8b60).
Report is 9 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff              @@
##             master      #43      +/-   ##
============================================
- Coverage     96.96%   94.11%   -2.86%     
  Complexity       11       11              
============================================
  Files             5        5              
  Lines            33       34       +1     
============================================
  Hits             32       32              
- Misses            1        2       +1     

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