This is a great idea, and would introduce a "Medic" class to ship design. Targeting a damaged ship (with it's design loaded) would show an "x-ray" type view of the ship, with missing/damaged blocks in red.
The addition of effects systems to the AstroTech is also a great idea! Perhaps support systems could be included too, so we can have a repair pulse, or lock on repair missiles!
I do like the x-ray vision idea! And lock-on repair missiles.. hahah. That would be hilarious.
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What if astrotechs only repaired / replaced hull and armor? Shipyards would then retain most of their usefulness.
I think that, just as in real life, there can and should be more than 1 way to do things. I don't think giving the AstroTech beam this functionality would make everybody want to stop using the shipyard. Here's why:
AstroTech:
Pro: Nothing is destroyed in repairing the ship
Con: You have to fly around and repair a ship with another ship that has AstroTech beams or build a complicated apparatus that would do it automatically.
Shipyard:
Pro: It's easy peasy to use. It's great for doing a complete rebuild of a ship.
Con: You have to take everything out of the ship storages, all the display modules are reset during the rebuilding process, all jump drives are emptied, and all logic systems are reset.
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I imagine a cargo ship, with the supplies, and one or more repair shuttles that can deploy from it. The cargo ship enters the sector, then a repair shuttle deploys, using the cargo ship as personal cargo.
For that matter, large ships could have there own repair supplies, and the repair shuttles just deploy from the mother ship.
I like the idea of being able to use personal storage for the astrotech beam. Perhaps it could work like a salvage beam, but in reverse. If connected to a storage, it uses that storage. If not, then it attempts to pull from the active inventory of a pilot, whether it is their personal inventory or personal cargo.