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That's true. Mostly it does it for "easy" upgrades, but the case where it's replacing a completely different file instead of an older version of the same script is pretty nasty.
These cases could be differentiated by looking for .conscript/sbt-launch.jar in the file. If that's not found, refuse to replace and let the user sort it out.
A prompt would be nice, or at least rename any existing files as a backup!
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