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Sadly no mention of I2P even though it was working quite well even back then. http://www.i2p2.de/

You can use Bittorrent in it, there is a emule port, gnutella etc. Works quite well. I often have download speeds of ~50Kilobytes/s in Bittorrent. It is a self-contained net with some trackers.

True, if I had more time I would have added I2P too. Since the thesis was only 12 out of 30 credits in that semester, I opted for looking at the anonymizing properties of 'regular' file-sharing software and software with anonymity as a main focus rather than looking at generic overlay networks too. This would have been the next step though :)

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