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Seems to be a JDT/UI feature
What version would that be, just an increment? On any resource modification.
Perhaps you could add automatic updating for the current whatever variables (e.g. current time, current file, current package) in the code templates? That would handle date-time versioning and keep javadoc correct across refactorings. It would be a separate RFE, but might do enough to cover this one too. With the above, you could make a build count variable available to the code templates, which would handle the incremented number versioning style.
I don't think we should go into this. There has to be some standard for that otherwise we do something that most other users don't like. I guess version numbers should also be in sync with version numbers from your repository. This feature is a good idea for an extra, additional plugin, that could be pioneered by somebody in the comunity.