No you should create the controllers folder under the project root, app_plugins is a special folder and contains content so will not get built.

I will ost some code later, not at home currently

Any chance you can share that code?

Unfortunately I can't currently get access (I'm in Spain and unable to get on my work VPN at the moment, however if you look at the page you linked to, everything you need is there, it is just not all in one place, so you need to read it all to work out what bits go where.

Basically you need to create the controller something like below (copied from example in the link

[Tree(SectionAlias = "settings", TreeAlias = "favouriteThingsAlias", TreeTitle = "Favourite Things Name", TreeGroup = "favouritesGroup", SortOrder = 5)]
[PluginController("favouriteThings")]
public class FavouriteThingsTreeController : TreeController
{ 
    protected override TreeNodeCollection GetTreeNodes(string id, FormDataCollection queryStrings)
    {
        var nodes = new TreeNodeCollection();

        // check if we're rendering the root node's children
        if (id == Constants.System.Root.ToInvariantString())
        {
            // you can get your custom nodes from anywhere, and they can represent anything...
            Dictionary<int, string> favouriteThings = new Dictionary<int, string>();
            favouriteThings.Add(1, "Raindrops on Roses");
            favouriteThings.Add(2, "Whiskers on Kittens");
            favouriteThings.Add(3, "Skys full of Stars");
            favouriteThings.Add(4, "Warm Woolen Mittens");
            favouriteThings.Add(5, "Cream coloured Unicorns");
            favouriteThings.Add(6, "Schnitzel with Noodles");

            // loop through our favourite things and create a tree item for each one
            foreach (var thing in favouriteThings)
            {
                // add each node to the tree collection using the base CreateTreeNode method
                // it has several overloads, using here unique Id of tree item, -1 is the Id of the parent node to create, eg the root of this tree is -1 by convention - the querystring collection passed into this route - the name of the tree node -  css class of icon to display for the node - and whether the item has child nodes
                var node = CreateTreeNode(thing.Key.ToString(), "-1", queryStrings, thing.Value, "icon-presentation", false);
                nodes.Add(node);
            }
        }

        return nodes;
    }

    protected override MenuItemCollection GetMenuForNode(string id, FormDataCollection queryStrings)
    {
        // create a Menu Item Collection to return so people can interact with the nodes in your tree
        var menu = new MenuItemCollection();

        if (id == Constants.System.Root.ToInvariantString())
        {
            // root actions, perhaps users can create new items in this tree, or perhaps it's not a content tree, it might be a read only tree, or each node item might represent something entirely different...
            // add your menu item actions or custom ActionMenuItems
            menu.Items.Add(new CreateChildEntity(Services.TextService));
            // add refresh menu item (note no dialog)
            menu.Items.Add(new RefreshNode(Services.TextService, true));
        }
        else
        {
            // add a delete action to each individual item
            menu.Items.Add<ActionDelete>(Services.TextService, true, opensDialog: true);
        }

        return menu;
    }

    protected override TreeNode CreateRootNode(FormDataCollection queryStrings)
    {
        var root = base.CreateRootNode(queryStrings);

        // set the icon
        root.Icon = "icon-hearts";
        // could be set to false for a custom tree with a single node.
        root.HasChildren = true;
        //url for menu
        root.MenuUrl = null;

        return root;
    }

}

I took your code and put it in a controller. Here is the complete code. This is to be put on a section called "Web Subscriptions", with an alias of "WebSubscriptions". I created a file called "WebSubscriptionsTreeController.cs" and put it in "~/controllers" folder. When I run the site and view the section, a blank tree panel flashes for a split second and then disappears. Do I need to register anything for this in the manifest?

using Bridge.Models;
using System;
using System.Collections.Generic;
using System.Linq;
using System.Web;
using System.Web.Mvc;
using Umbraco.Web.Mvc;

namespace Bridge.Controllers
{
[Tree(SectionAlias = "WebSubscriptions", TreeAlias = "WebSubscriptions", TreeTitle = "Web Subscriptions", TreeGroup = "favouritesGroup", SortOrder = 5)]
[PluginController("Websubscriptions")]
public class WebSubscriptionsTreeController : TreeController
{
    protected override TreeNodeCollection GetTreeNodes(string id, FormDataCollection queryStrings)
    {
        var nodes = new TreeNodeCollection();

        // check if we're rendering the root node's children
        if (id == Constants.System.Root.ToInvariantString())
        {
            // you can get your custom nodes from anywhere, and they can represent anything...
            Dictionary<int, string> favouriteThings = new Dictionary<int, string>();
            favouriteThings.Add(1, "Raindrops on Roses");
            favouriteThings.Add(2, "Whiskers on Kittens");
            favouriteThings.Add(3, "Skys full of Stars");
            favouriteThings.Add(4, "Warm Woolen Mittens");
            favouriteThings.Add(5, "Cream coloured Unicorns");
            favouriteThings.Add(6, "Schnitzel with Noodles");

            // loop through our favourite things and create a tree item for each one
            foreach (var thing in favouriteThings)
            {
                // add each node to the tree collection using the base CreateTreeNode method
                // it has several overloads, using here unique Id of tree item, -1 is the Id of the parent node to create, eg the root of this tree is -1 by convention - the querystring collection passed into this route - the name of the tree node -  css class of icon to display for the node - and whether the item has child nodes
                var node = CreateTreeNode(thing.Key.ToString(), "-1", queryStrings, thing.Value, "icon-presentation", false);
                nodes.Add(node);
            }
        }

        return nodes;
    }

    protected override MenuItemCollection GetMenuForNode(string id, FormDataCollection queryStrings)
    {
        // create a Menu Item Collection to return so people can interact with the nodes in your tree
        var menu = new MenuItemCollection();

        if (id == Constants.System.Root.ToInvariantString())
        {
            // root actions, perhaps users can create new items in this tree, or perhaps it's not a content tree, it might be a read only tree, or each node item might represent something entirely different...
            // add your menu item actions or custom ActionMenuItems
            menu.Items.Add(new CreateChildEntity(Services.TextService));
            // add refresh menu item (note no dialog)
            menu.Items.Add(new RefreshNode(Services.TextService, true));
        }
        else
        {
            // add a delete action to each individual item
            menu.Items.Add<ActionDelete>(Services.TextService, true, opensDialog: true);
        }

        return menu;
    }

    protected override TreeNode CreateRootNode(FormDataCollection queryStrings)
    {
        var root = base.CreateRootNode(queryStrings);

        // set the icon
        root.Icon = "icon-hearts";
        // could be set to false for a custom tree with a single node.
        root.HasChildren = true;
        //url for menu
        root.MenuUrl = null;

        return root;
    }

}
}

This is just a thought as I don't know for sure (I will try out your code tomorrow)

It could be because your section and tree share the same alias.