When adding one or more breakpoints to a VI, the user is asked to save the VI when closing it even in the case that he has already removed the breakpoints again manually or with the breakpoint manager. When using sourcecode control like TortoiseSVN, this makes always trouble when closing a larger batch of VIs and no time to look which VI has been really changed and which not. Because then you will save a new version of a VI which has not been changed at all. You have to click around a lot to not get into these conflicts.
Saving breakpoints with a VI might be a helpfull option for some developers (not for me, I have never had the need to save breakpoints with a VI).
Nevertheless my suggestion is that the version status of a VI should not be changed when adding breakpoints, or at least should be reseted when the breakpoints have been removed again.
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