Update Base, ToolBase, and other dependencies

[alexander-yevsyukov]

This PR applies latest config, thus updating internal and external dependencies. Related deprecations and API changes were addressed.

Notable changes

• The BomsPlugin was applied to the modules.
• JavadocConfig was applied to the modules avoiding numerous warning errors emitted by the Javadoc task in the generated Protobuf code.
• The javadoc task now runs only in production modules.
• The io.spine.gradle.javadoc package was a bit simplified by moving TaskContainer extension functions under the JavadocConfig.kt file.
• Testing configuration per module now is done by module-testing conventions plugin.
• Console output was tapped in LoggingLevelSpec test which tests setting the DEBUG level via command line parameter.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.52%. Comparing base (2ef601e) to head (2a2af04).
Report is 17 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff              @@
##             master     #350      +/-   ##
============================================
- Coverage     74.82%   74.52%   -0.31%     
+ Complexity      615      613       -2     
============================================
  Files           196      197       +1     
  Lines          4254     4294      +40     
  Branches        396      397       +1     
============================================
+ Hits           3183     3200      +17     
- Misses          938      965      +27     
+ Partials        133      129       -4     

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