I am using Bundlor via Maven and via Eclipse. There is an issue I discovered between the two approaches to generate the MANIFEST.MF. The Maven plugin either manipulates the packaged artifact directly (via transform) or creates in the configured output folder (via manifest). Thus you always have an up to date MANIFEST.MF in your resulting artifact and don't need to check a MANIFEST.MF into the VCS of choice.
The Bundlor Eclipseplugin relies on the existence of a MANIFEST.MF in one of the source folders (as it probably can not be sure where to put a newly created one?). So I have to create a MANIFEST.MF file myself and put it into let's say src/main/resources. If I want my college to be able to work with the project out of the box I have to check this file into the VCS, which is rather suboptimal as - that is bigger issue IMHO - you have a MANIFEST.MF in the project sources that might differ the one that ends up in the artifact (if you build with Maven).