plugins and their scope

Not much info is written on plugins right now. It seems like they are intended to be used only at the application-level, and for things like emitting multiple files (factor-bundle being a good example).

But they don't have "full control" over the bundler like you may need for an application-specific plugin. For example, to override or disable transforms across module dependencies.

Shouldn't the plugins be the first thing that are instantiated on the bundler, rather than the last? And, further, shouldn't the plugin features also trickle down to the dependencies handled by module-deps? Or am I misunderstanding the goal of these plugins?