Modernise the build: move root `build.gradle.kts` setup into the `module` script plugin

[alexander-yevsyukov]

Goal

Adopt the module script-plugin approach used by the recently modernised Spine
repositories (base-libraries,
core-jvm,
compiler, …) so that each subproject is
configured by plugins { id("module") } (or id("jvm-module")) instead of a large block of
imperative per-project setup in the root build.gradle.kts.

Current state

The root build.gradle.kts is 557 lines, most of it per-project
configuration applied from a subprojects { … } block through hand-rolled Project
extension functions:

• applyPlugins() — applies java-library, org.jetbrains.kotlinx.kover,
  com.google.protobuf, net.ltgt.errorprone, kotlin, pmd, maven-publish,
  pmd-settings, dokka-setup, io.spine.core-jvm, plus IncrementGuard, BomsPlugin,
  and license / Javadoc / Checkstyle configuration.
• setupJava(), setupKotlin(), setupTestTasks(), defineDependencies(),
  applyGeneratedDirectories(), forceConfigurations(), setupPublishing(),
  configureTaskDependencies().

This re-implements, by hand, the build contract the organisation now centralises in
convention plugins — so every change to that shared contract has to be re-applied here
manually, and the root script drifts from the other repos.

Target

• Move the per-module setup into the module / jvm-module script plugin. The repo
  already ships buildSrc/src/main/kotlin/module.gradle.kts — the project-owned module
  convention plugin (it is the explicit buildSrc/** exception in AGENTS.md), which is
  the natural landing spot.
• Each subproject's build.gradle.kts shrinks to plugins { id("module") } plus its own
  dependencies.
• The root build.gradle.kts keeps only genuinely root-level concerns — aggregation
  (KoverConfig, LicenseReporter, PomGenerator), spinePublishing, repositories — and
  drops the subprojects { } setup-function machinery.
• Mirror the structure of base-libraries / core-jvm / compiler.

Notes

• The recent JaCoCo → Kover migration was applied inside applyPlugins(); the
  module / jvm-module plugin already auto-applies Kover, so this refactor absorbs that
  change rather than conflicting with it.
• Build-only refactor — no production or test code changes; coverage, publishing, and
  report outputs must stay equivalent.