Annotation index: avoid iterating the same URL twice

When a URLClassLoader has a class path element that the parent class
loader also has, ClassLoader#getResources() will list it twice. Work
around that.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Annotation index: Add a unit test for repeated class path elements

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>