My suggestion is that nuget package version numbers should be independent of the assemblies'. For example, when I started to publish packages for the open source projects I manage,
http://nuget.org/profiles/lextm
http://nuget.org/profiles/lextm
- The assembly version number strictly follows Microsoft's approach on Visual Studio (as I use AssemblyInfo Task). The four-part format is meaningful for the developers to handle bug reports, but I think the last two parts are meaningless to the users. So for the nuget packages I only keep the first two parts the same as the assemblies.
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I noticed that sometimes I need to patch the nuget package alone (keep the binaries unchanged) because I missed something in the release notes, or I set a property wrongly, or I forgot to keep the framework hirarchy properly. In those cases I simply perform repackaging, and increase the fourth part (so get ..0.1). Well, in the future I might follow the SysVer recommendation to increase the third part.