I've created a p2 mirror as described in various places:
I've filled it with the bundles for Eclipse 3.7. It now contains stuff like ECF and the C++ tools which I won't need.
What is the best way to clean those from a repo? Can I remove them at all or do I have to run the mirror script again using a partial mirror?
You can use p2.remove.iu
Ant task. Look for this and other useful p2 repository tasks here.