[KARAF-2951] Transitive repositories and bundles are not added to system repo

commit fd0143a1e4895dfc8af04efd33ec3445b9278f00 backported to karaf-3.0.x branch
Hi,
If this line is changed to the following lines, the features from the innerRepository don't get lost:

```java
Features innerFeatures = loadAndCopyRepo(URI.create(innerRepository));
features.getFeature().addAll(innerFeatures.getFeature());
```