The darker blue circle around a ship means it's cloaked.
Also blue lines are Cloak Boosters, which only the scout ships have, but they boost any cloaked unit, including remains rebuilders, cleanup drones, etc.
A cloaked ship that is cloak boosted by another ship cannot be decloaked by tachyon drones. Note that this is limited somehow, I think it's that if a ship is cloak boosting another ship, it cannot itself be cloak boosted, but I'm not 100% on that.
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The green lines are engineers repairing something (healing/building it). Those lines will go red if the engineer can't repair it for some reason, but is assigned to it ongoing.
The blue lines are tractor beams, and hold stuff in place.
The yellow lines are tachyon beams, and reveal stuff that is cloaked.
You can't rebuild enemy stuff, you'll want to use cleanup drones on that. Rebuilders are for your own stuff.