When resolving dependencies with importRuntimeDependencies and adding them to an archive as in

File[] libs = Maven.resolver().loadPomFromFile("pom.xml").importRuntimeDependencies().asFile();
ShrinkWrap.create(WebArchive.class, "seam-blog.war").addAsLibraries(libs);

system-scoped dependencies are resolved and added to the archive as well.

This should not happen and should be aligned with the behaviour of the maven war plugin, as described in this issue: https://jira.codehaus.org/browse/MWAR-23.