The interactions between autojunction and abutted co-linear lines has always been a problem in P99SE - it leaves stray autojunction hot spots around the design. But John seems to have a different problem. If as John Elson points out, the presence of the auto-junction is essentially visual where you have a wire crossing abutted wire - then this is a problem. If I understand John E. correctly he is saying that if you have the conditions for an autojunction but you don't have the autojunction there (either autojunction is not enabled or you delete the junction), you may still have the connection in some circumstances. This is a pretty dangerous situation - it is interesting though that it has not come up a lot over the last 4 year.
Leaving autojunction enabled will help. At least then you may see stray connections - if you or a reviewer happens to notice them.
(DXP comment - DXP offers some help here. Firstly wire segments have little graphical details to show where they end. So if you do have two abutting wire segments you can see this little detail. Secondly, there is an option to optimise wires - this option will merge co-linear abutted line segments. This optimise option also offers a nice feature where is you drop a two wire component onto a wire the wire will be split into two nets at the two pins (you can drop in a series resistor, for example easily. As near as I can figure, after discussing this issue of merging line segments for years, the optimise function was added to DXP after I pointed out that you could draw a wire on a DXP sample schematic between two particular points and end up with stray auto-junction hot spots. I am not sure why but it seemed that the discussion in PEDA about this issue for years had not quite managed to make it into the required DXP feature list. Only after the problem was easily demonstrated in a Altium sample Sch did it become apparent why something should be done.)
Hey John B. - if you do evaluate alternative packages why don't you report here. Especially after a few projects on the new one.
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