We currently do not support setting how the version string is displayed in the URL, unfortunately.
This is a link to a problem on our codeplex website: Url version issue
In the meantime, if you want to live with manually changing the package path every time you change the package, you can simply avoid using helpers and just have explicit links to your packages that you update every time your package changes:
<link href="/Content/themes/base/css" rel="stylesheet">
Or you can disable client caching using bundle.Cacheability = HttpCacheability.NoCache
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