Had this problem:
Cannot resolve dependencies for the following module(s)
EPiServer.Cms.Shell.UI.InitializableModule
EPiServer.Cms.Shell.UI.InitializableModule
EPiServer.Web.InitializationModule
EPiServer.Web.InitializationModule
Turns out the C:\Program Files\EPiServer\CMS\6.0.530.0\bin doesn’t contain all the necessary dlls.
instead you can either do a clean install and steal the dlls from that site’s /bin or you can fetch them from C:\Program Files\EPiServer\CMS\6.0.530.0\VSTemplates\EPiServerProject.zip
(thanks Jamie Dixon: http://www.jamie-dixon.co.uk/episerver/upgrading-episerver-to-version-6/ )

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