I would also like to rekindle my support for this idea. Transports with 5k capacity used for PoB supplying that want to save an extra trip per commodity type have no choice but to eschew armor upgrades. In that case, it's less about being greedy with the extra 20 cargo space and more about simply wanting to save time in building PoB created equipment. Since many people own bases solely for the purpose of producing equipment for other players to enjoy, I feel that it would be a big boon for transports to have their nanos merged into their hulls.
Not to mention, repair ships would see a nice buff, since the Nano-Tool repairs a % of the target's total health, rather than a static number.
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