Don't skip trees with transparent positions when looking for references

Trees with a transparent position may contain trees with range
positions, hence we should make sure to:

1) Traverse tree with a transparent position, and
2) Only call `report` on tree that have an opaque range position.

This is a bug that was made apparent by the changes needed to fix the
Scala compiler ticket SI-4287.
Merge pull request #606 from dotta/issue/si-4287

Don't skip trees with transparent positions when looking for references