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1,2 You can update class names and java files using Refactor/Rename in the menubar and popup menu. Refactoring updates the class name, file name to match and updates all of the references to the class in your source code.
Check here for more hints https://netbeans.apache.org/kb/docs/java/index.html
3 I dont know much about Gradle but those are simply default project names applied to files created when you create a new project. You can create custom names when you create a new project.
4 Yes, Ant, Maven and Gradel all handle the same basic tasks but in different ways. Consult the manual for each build tool on the internets.

HTH,
Ed

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@valmirserpa
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