Plugin class code is necessarily part of the overall plugin assembly, so you have to deploy the whole assembly to deploy code changes.
However, if the other classes have not changed, how much of a problem is it to update them when you deploy the assembly ?
If you do need to deploy individual plugin classes separately, then you'd have to split them into different assemblies. This should be possible with the Developer Toolkit, though I think it would take some effort to change an existing environment,
as I think the plugin classes will get new primary keys, so all plugin steps would need to be recreated
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