Fix issues in GradleJpsSyncExtension

[akerimsenol]

Note

Generalizes duplicate URL pruning to ContentRootEntity, SourceRootEntity, and ExcludeUrlEntity with shared-source-aware logic, replacing the previous content-root-only approach.

• Gradle JPS Sync:
  • Replace removeDuplicatedContentRoots with a generic removeDuplicatedUrlEntities<T> that de-duplicates by (url, module).
    • Applies to ContentRootEntity, SourceRootEntity, and ExcludeUrlEntity.
    • Uses shared-source-aware keys: allows duplicates across modules when shared source support is enabled, but removes duplicates within the same module.
  • Minor imports and helpers added (e.g., VirtualFileUrl, Project, and sharedSourceSetAware).

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[nskvortsov]

Please add test covering this change

[akerimsenol]

Added test cases in GradleJpsSyncExtensionTest. Please take a look.