I have just released completed work on STSDev 2008 Version 2.0.1 which provides a number of fixes to the original 2.0 version.
Fixes
In STSDev 2008 the attempt was made to read through the project file and find all the “dependent” assemblies so they could be deployed with the solution. This lead to a number of issues when trying to find those assemblies, so in STSDev 2008 v2.0.1 only assemblies in the build output folder are included in the Manifest.xml file. This allows developers to “choose” what assemblies to deploy in their solution simply by setting the “copy local” option on your reference assembly. Once the assembly is copied to your build output folder STSDev 2008 will include it in your solution.