I package my Maven-based Spring app with:
mvn install-DskipTests -Peverything.
And something strange arises. In META-INF of generated jar,
It seems like this is a somewhat common problem that arises from a conflict in Eclipse, especially with the m2e-wtp integration.
Some people are indicating that it can be fixed by including clean in the list of goals to run, e.g. mvn clean package.
Also try to update your m2e installation and make sure you don't have multiple versions of m2e or m2eclipse (the pre-Indigo version) installed.
Some references to other people facing this problem: