We just added a Post-build event command line in the settings for the project similar to this (this places the newly bundled version of the addin in a sub-folder named "Bundle" in the TargetDir of the project :
c:\<path to ilmerge.exe> /lib:C:\<path to folder containing add-in & Newtonsoft.Json.dll> /lib:C:\<path to folder containing RevitAPI libraries> /t:library /out:$(TargetDir)Bundle\<Name of your addin>.dll <New name for bundled addin>.dll Newtonsoft.Json.dll