since uprading to Virgo Tooling 184.108.40.206302081934-SNAPSHOT I get empty manifests when deploying within Eclipse. The manifest files are correctly generated in the Eclipse project, but the ones copied to the stage directory just contain a header:
Built-By: john doe
Created-By: Maven Integration for Eclipse
Do you have a sample that reproduces the issue? Also, what tool is generating your Manifests? The "Created-By: Maven Integration for Eclipse" suggests to me that you're using some sort of Maven Bundlor integration instead of the Virgo IDE Bundlor integration maybe?