I am using STS to build a web application for DM server. My src directory is src/main/java for java source code, and src/main/webapp for web code (just as maven defines). I also define a template.mf, but anytime the auto-generated MANIFEST.MF goes to src/main/java/META-INF, I want it in src/main/webapp/META-INF/. Bundlor will create directory src/main/java/META-INF.

Any idea?