chore(infra+frontend): upgrade Gradle to 9.3.1 and fix KMP plugin conflicts in Docker builds

- Updated Gradle version in `.env`, Dockerfiles, and wrapper to 9.3.1.
- Replaced alias-based application of `kotlinMultiplatform` plugin with direct `id` usage in subprojects to resolve "Plugin loaded multiple times" error.
- Applied centralized plugin management and Gradle daemon optimizations to improve Docker build stability and address KMP classloading issues.

frontend/core/sync/build.gradle.kts

@@ -1,5 +1,6 @@
 plugins {
-  alias(libs.plugins.kotlinMultiplatform)
+  // Fix for "Plugin loaded multiple times": Apply plugin by ID without version (inherited from root)
+  id("org.jetbrains.kotlin.multiplatform")
   alias(libs.plugins.kotlinSerialization)
 }