As I look at the following code, I easily can conclude problems on Windows.
The problematic snippet is .replace(File.separatorChar, '/'). On any other environment that Windows this might work but it does not work with backslash file separators.
At first classesDir is compared to ourRsrcPath which is correct as both values have their slashes replaced. The second comparison on line 545, however, is invalid because rsrc.getDirectory() contains native file separators when compared to ourRsrcPath with replaced file separators.
As a consequence, the outputDirecory becomes (is added as a) maven project resource and everything inside it if previously existing is copied into the target directory. In my case I specified the project root directory as outputDirectory so that Eclipse PDE finds the OSGI-INF folder in the place expected and added the root folder with an inclusion pattern of OSGI-INF/** to the project resources. The issue caused the whole project to get copied into the target/classes folder resulting in something like target/classes/target/classes, which maven-bundle-plugin is then complaining with an error because: