Solution Aware Plugins - rezanid/xrmtools GitHub Wiki
When you run Register plugin(s) command, by default all the registrations will go to your preferred solution in the current Dataverse environment. You can change this behavior by manually setting the solution for the project that contains your plugins. In order to do that, add the following assembly scoped attribute:
[assembly: Solution("Unique-Name-Of-The-Solution")]
Perhaps the best place to add this attribute is the AssemblyInfo.cs file that you can find under Properties folder of your project in the Soltution Explorer.