Hi Mateusz, in nexus 1.3 we started using the new .gz index format, although nexus isn't currently able to download the incremental index portions, it can download (and properly process) the full .gz index that is now being published by nexus (and the nexus-indexer) or the .zip legacy file that is available in places that use pre-2.0.0 indexer.
So the .gz extension isn't directly tied to supporting incremental updates. When you reindexed your public group earlier, did you wait for the reindex to finish before attempting to download with m2eclipse again, and did the task complete successfully (you can check via the System Changes in feed in the UI) ? I'm just curious if the reindex task wasn't yet complete or failed.
Thanks
Damian