Redmine

Well, I don't get the point what breaks your plugin.

Do you use a ul/li inside the ul/li of the sidebar?

Maybe it would be enough to change #sidebar ul to #sidebar > ul

Yes, the plugin imports a tree structure into #sidebar.

Well, it has a very complicated css rendering by js.

I only suggest, I do not insist.

Can you try to change

#sidebar ul to #sidebar > ul
and
#sidebar ul li to #sidebar > ul > li

I think this should do the trick and we don't need to add another class to the css. :-)

Do you mean in application.css?
If so, it will not, whereas there are <ul>'s situated in <form> and only after that in <div id="sidebar"> in some places.