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GH-40843: [Java] Cleanup protobuf-maven-plugin usage (#40844)

### Rationale for this change

`protobuf-maven-plugin` usage in Arrow codebase does not follow plugins best practices like sharing the same output directory for different execution or not using test goals for generating test classes

### What changes are included in this PR?

* Add protobuf-maven-plugin plugin to top level pom.xml under pluginManagement to define version and common configuration for all modules
* Remove unnecessary executions of test-compile goal when no test protobufs are present
* Remove use of outputDirectory and clearOutputDirectory and let the plugin choose it for each execution (the default output directory is based on the phase (main vs test) and the language/plugin-id)
* Replace use of compile/compile-custom goals with test-compile/test-compile-custom when generating test protobufs

### Are these changes tested?

As those changes are in the build system, they are covered by the build framework and tests run as part of the build

### Are there any user-facing changes?
None
* GitHub Issue: #40843

Authored-by: Laurent Goujon <laurent@apache.org>
Signed-off-by: David Li <li.davidm96@gmail.com>