You have a rather awkward set up where a maven driven build and a Bnd Workspace model build set in the same folders. You should pick either a maven drive build and use the bnd Maven plugins or you should pick a Bnd Workspace model where bnd drives the build (using gradle for command line building).
Maven builds are laid out differently than Bnd Workspace builds. For example, maven puts java source in src/main/java and resources in src/main/resources. Bnd Workspace builds put src and resources together in src.
Since you would seem to prefer maven-driven builds, you should use m2e with Eclipse and the bnd maven plugins (bnd-maven-plugin is the main plugin) to make your bundle jars in maven. Then you can remove all the gradle things which are for Bnd Workspace model builds.