Eclipse maven-jar-plugin not signing, because of duplicate entries pom.xml and pom.properties only on Windows
This is the solution by the question's author, moved to the appropriate section.
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So I found it out myself. Here is what helped me to fix the problem.
Research
I found this question after more research and they stated, that the maven.archiver is the cause, because it wants to create the both files after they have been copied into the jar from m2e.mavenarchiver-plugin.
"... the m2e.mavenarchiver is creating pom.xml files etc. in the target directory, then these get pulled in by the maven archiver maven plugin, which then also creates its own files - hence the duplicates."
So the solution is also stated on this topic site.
Solution
Add
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<addMavenDescriptor>false</addMavenDescriptor>
</archive>
</configuration>
</plugin>
to your pom.xml