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Multiple Assemblies

I’m using SmartAssembly Version 6.1 and I’m trying to automate my build process using msbuild. So far, I’m confused as to how the whole thing works given my special case. My application isn’t one giant assembly, but it consists of a solution file with multiple project files:
  • Application
      Depends on :
      DataModel PluginsInterface Support 3rd Party Logging Apparatus
[/*]
[*] DataModel[/*]
[*] Plugin
    Depends on:
    PluginInterface 3rd Party Logging Apparatus
[/*]
[*] PluginInterface
    Depends on:
    3rd Party Logging Apparatus
[/*]
[*] Support[/*]

I want to obfuscate every assembly then merge or embed the components together such that at the end of the build there should be two files:
    Application Plugin
I also want to make sure I'm not including duplicate assemblies in to my final build such as the 3rd party Logging. How would I setup my MsBuild to handle this situation? Do I have to create a separate project file that obfuscates each assembly then perform the merging at the application project?
    JohnRedGater
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