I found a way to dock a plugin using the reposition api. See it in use in my Plugin for Translation managment - Parrot.
Sadly there is a bug in the reposition function in Figma and there is no easy and robust way to get the xy position of the plugin atm - see Retrieve plugin UI position? and Get relative position of plugin UI window to main Figma window
So the solution i come up with involves a lot of little tricks. I am currently cleaning up the code and plan to publish it as a little library soon.
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