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You are right, but it's not a simple thing to fix. Sometimes, layers can share the same set of coordinate data, for example, if they are derived from the same source layer, or if a group of files are imported together, using the combine-files flag. Certain commands will modify the coordinates of all layers in the group, even if you only specify one of the layers as a target. -simplify and -proj work this way, and so does -snap. Most of the time this is the behavior that I want... but this behavior can also take users by surprise. I haven't figured out how to explain the layer grouping concept to users in a clear and simple way. I welcome any suggestions that you have.
Snap effects layers with the same source, even if the target is explicitly specified with target=
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