Cut and paste a block of schematic containing wire junctions. Observe strange floating junctions shown in screen shot.
Application: Eeschema
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I'm not sure if this is the right place to talk about this, but I find the concept of independent junction dot weird. Junction should be a property of two or more wires crossing (or endpoints touching, or endpoint touching another line) and there shouldn't exist any junction without two wire lines.
From the standpoint of implementation it may be easier to have separate junctions but they should very strictly depend on existence of a wire crossing. For example, instead of
junction: xcoord,ycoord
there could be
junction:
wire: id
wire: id
But at least, if they are separate independent entities, they should be updated very stricly with any change made to wires. The update mechanism should be "waterproof". I've seen different situations when junction don't correctly reflect changes made to the wires.
It shouldn't be possible to add junctions where there are no wires crossing, and there should never be need to remove junctions except from where wires are crossing. "Add junction" shouldn't blindly add a junction dot, it should only make a junction out of two wires crossing each other.