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1) Spawn Anvil Asgard (as an example but this is a general issue)
2) Spawn ATLS
3) Try to load 32x 4-SCU boxes onto the Asgard cargo grid using the ATLS

What happened
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The ATLS can typically load the bottom 2 cargo layers just fine. Layer 3 tends to work with some extra care but isn't as smooth as 1-2. Layer 4 (top) of the cargo cannot be loaded with an ATLS as it mindlessly shoves the boxes into the layer below, trying (and failing) to force them through, rather than lifting them to the proper height first and then sending them where they should go.

What should have happened
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ATLS tractor functionality is generally quite fragile and really needs proper 'smart pathing' added so boxes are actually reliably sent to their destination, so long as a viable clear path exists between the box, the ATLS and the destination, rather than trying to shove them through some other box or piece of wall.

Workaround
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No workaround with the ATLS itself as the issue persists regardless of angle or distance. Only workaround is to not use an ATLS at all and switch to Maxlift or Multi-Tool which obviously defeats the purpose of the ATLS.