Patch Set 1:

I tried with the shared library in the bundle root as well but this didn't fix the problem.

One strange thing I observed : I found that the manifest entry for
the native code

Bundle-NativeCode: /native/macosx/x86_64/libjgitnative.jnilib;
	 osname=macosx;
	 processor=x86_64;

has to end with a semicolon, but the OSGi spec says this should not be necessary. When removing the semicolon I get an error message that the bundle Bundle-NativeCode_0.0.0 cannot be resolved. Maybe this points at a bug. With the manifest as posted here org.eclipse.jgit can't load the JNI class in the native fragment so I am seeing ClassNotFoundException.