New ProtoData, Base, Dependency object API, etc.

[alexander-yevsyukov]

This PR pulls config updating major local dependences and external dependencies. Protobuf was bumped to 3.25.7, which is the latest version in the 3.x family.

Notable changes

• Annotations were migrated to JSpecify.

Build changes

• module-testing and BomsPlugin were applied to the module conventions plugin.
• Several artifacts adopted the new Dependency and DependencyWithBom API which helps in defining dependencies with multiple artifacts and BOMs.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 31.97%. Comparing base (25d2a2e) to head (e93e585).
Report is 20 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff              @@
##             master     #221      +/-   ##
============================================
- Coverage     32.04%   31.97%   -0.07%     
+ Complexity      238      233       -5     
============================================
  Files           128      128              
  Lines          2896     2896              
  Branches        208      208              
============================================
- Hits            928      926       -2     
- Misses         1916     1917       +1     
- Partials         52       53       +1     

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