Streamline logging dependencies

[koppor]

Triggered by JabRef/jabref#10046

We start to use GemFX in our project:

+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.74.0') {
+       exclude module: 'javax.inject' // Split package, use only jakarta.inject
+       exclude group: 'org.apache.logging.log4j'
+    }

Dependency inclusion of gemsfx should not require playing around with logging. Thus, I checked the code. The code itself uses JDK's logging framework. Only the dependencies do make use of some logging. Therefore, I removed the direct logging library requirements.

I also removed two duplicated entries in pom.xml.