build(deps): bump protobuf from 3.25.5 to 4.31.1

Bumps `protobuf` from 3.25.5 to 4.31.1.

Updates `com.google.protobuf:protobuf-java` from 3.25.5 to 4.31.1
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Changelog](https://github.com/protocolbuffers/protobuf/blob/main/protobuf_release.bzl)
- [Commits](protocolbuffers/protobuf@v3.25.5...v4.31.1)

Updates `com.google.protobuf:protobuf-java-util` from 3.25.5 to 4.31.1

Updates `com.google.protobuf:protoc` from 3.25.5 to 4.31.1
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Changelog](https://github.com/protocolbuffers/protobuf/blob/main/protobuf_release.bzl)
- [Commits](protocolbuffers/protobuf@v3.25.5...v4.31.1)

---
updated-dependencies:
- dependency-name: com.google.protobuf:protobuf-java
  dependency-version: 4.31.1
  dependency-type: direct:production
  update-type: version-update:semver-major
- dependency-name: com.google.protobuf:protobuf-java-util
  dependency-version: 4.31.1
  dependency-type: direct:production
  update-type: version-update:semver-major
- dependency-name: com.google.protobuf:protoc
  dependency-version: 4.31.1
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Author: dependabot[bot]

gradle/libs.versions.toml

@@ -15,7 +15,7 @@ jspecify = "1.0.0"
 junit = "5.13.4"
 picocli = "4.7.5"
 protobuf-plugin = "0.9.5"
-protobuf = "3.25.5"
+protobuf = "4.31.1"
 reflections = "0.9.12"
 scala-library = "2.12.16"
 scalatest = "3.2.18"