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It seems to me that bug numbers ought to be associated with source files, however they are kept. Then, bug tracking systems could query the source control system for the information as needed.
Yeah, it seems like that should be the case. But...
A company I worked at changed from CVS (free, open-source, multi-platform) to StarTeam (expensive, proprietary, Windows-only) largely for the sake of the "match change requests to the source revisions that resolved them" feature. In the three years I worked there, nobody ever used this feature.
IMHO, this is the most overrated bug tracking concept out there, but most people won't believe that until they try it and realize that it's vastly more trouble than it's actually worth.
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