Update dependencies and migrate to Gradle 9 / Dokka v2

Dependency bumps: Kotlin 2.3.20->2.3.21, Coroutines 1.10.2->1.11.0,
Ktor 3.4.2->3.5.1, KSP 2.3.6->2.3.9, MicroUtils 0.29.2->0.30.0,
Dokka 2.0.0->2.2.0, Versions plugin 0.53.0->0.54.0, NMCP 1.4.4->1.6.0.

Gradle wrapper 8.13->9.6.1 with build-script fixes for Gradle 9:
Project.exec() -> providers.exec(), tasks.whenTaskAdded -> tasks.configureEach.

Dokka migrated to the Dokka Gradle Plugin v2. The docs module is now
included as the KDocs aggregator (dokka {} DSL with sourceRoots, new URI,
ProcessIsolation heap for the generator worker), excluded from binary
compatibility validation, and the kdocs workflow runs :docs:dokkaGenerate.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.6.1-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip