I package my Maven-based Spring app with:
mvn install-DskipTests -Peverything.
And something strange arises. In META-INF of generated jar,
Not sure what you mean by duplicate but the jar created by maven does come with pom.xml and pom.properties in META-INF folder. See this section of the maven getting started guide.
duplicate
pom.xml
pom.properties
META-INF