How do I avoid having duplicate of plugin in trunk?

I do not know which OS and/or software you use but regarding SVN it’s quite simple :

$ svn co http://plugins.svn.wordpress.org/your-plugin-name

Then you just have to add your files in trunk and/or maybe in assets (banner,screenshots).
Then :

$ svn add trunk/*

and or :

$ svn add assets/*

Last step is :

$ svn ci -m "initial upload"

That’s pretty much what I use to release plugins on wordpress.org, hope this will help 🙂