I dislike that feature very much. Yes, it is useful occasionally (rarely), but way more often, it is just annoying.
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I usually don't want stops (traces) to survive.
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I can make a working dir dirty (from Git's point of view) by setting a stop vector, making a change, undo the change and then fix the code.
I certainly don't want that, and I cannot imagine that anybody wants this.
Because Link records stops and traces in the config file I cannot add it to .gitignore either, so no easy escape route.