manifest.mf is overwritten by eclipse during jar export

While exporting the jar, select the option to use existing manifest and browse to the manifest file of your project. The generated jar will have that manifest file now.

Using existing manifest http://img46.imageshack.us/img46/6752/export.png

Using Oxygen (Release 4.7.0), I was able to do this successfully. The confusing part is that on the JAR File Specification page of the JAR Export wizard, both the Next and Finish buttons are active. So if you don't notice that and just click Finish, you'll end up with a warning (and the generated manifest). To use your own, click Next instead (once for JAR Packaging Options, and again for JAR Manifest Specification).