It appears to me that if I just invoke manifest goal of maven-bundle-plugin, it ignores _include instruction, where as if I use bundle goal, it is used by the plugin. There are various ways to test it. The easiest seems to be using a non-existent file name. Attached are two sets of pom files, pom.xml uses bundle goal, where as pom.xml.notworking uses manifest goal. While using the first one, bnd complains about missing osgi.bundle3 file, where as it does not report any such error while using the first one. That makes me think that the manifest Mojo is not sending the file name to bnd.
I am attaching a very simple test case along with a README describing the issue.