With the newer version of maven-bundle-plugin (previous release used 1.4.0, current is 2.1.0, but the parent-pom-eclipse-plugins is using 2.0.1 which was the current version when that pom was made), the generated Manifest is more detailed. However it is broken - inside the generated MANIFEST.MF, he org.eclipse.core.runtime import is declared now with the additional clause registry=split.
This affected several plugins, including in the core, the uimaj-ep-configurator, the uimaj-ep-debug, and uimaj-ep-jcasgen plugins.
The result: the update site would build, and would install, however, when attempting to run the plugins, they would fail with class-not-found exceptions.
The fix: it would work to go back to 1.4.0. But a better fix is to change the instructions to handle split packages better: Add the bundle org.eclipse.core.runtime to the Require-Bundle instructions, and add its negation, (!org.eclipse.core.runtime) to the Import-Package instruction, as required by OSGi.
While there, check the other negations to insure they are correct. The Require-Bundle clause takes a bundle-id, which by convention only is often the package name.