I encountered the same issue after updating the maven-jar-plugin to its latest version (at the time of writing), 3.0.2.
Eclipse 4.5.2 started flagging the pom.xml file with the org.apache.maven.archiver.MavenArchiver.getManifest error and a Maven > Update Project.. would not fix it.

Easy solution: downgrade to 2.6 version
Indeed a possible solution is to get back to version 2.6 , a further update of the project would then remove any error. However, that's not the ideal scenario and a better solution is possible: update the m2e extensions (Eclipse Maven integration).

Better solution: update Eclipse m2e extensions
From Help > Install New Software.. , add a new repository (via the Add.. option), pointing to the following URL:

  • https://repo1.maven.org/maven2/.m2e/connectors/m2eclipse-mavenarchiver/0.17.2/N/LATEST/

Then follow the update wizard as usual. Eclipse would then require a restart. Afterwards, a further Update Project.. on the concerned Maven project would remove any error and your Maven build could then enjoy the benefit of the latest maven-jar-plugin version.

Additonal notes
The reason for this issue is that from version 3.0.0 on, the concerned component, the maven-archiver and the related plexus-archiver has been upgraded to newer versions, breaking internal usages (via reflections) of the m2e integration in Eclipse. The only solution is then to properly update Eclipse, as described above.
Also note: while Eclipse would initially report errors, the Maven build (e.g. from command line) would keep on working perfectly, this issue is only related to the Eclipse-Maven integration, that is, to the IDE.