Bind Dictionary with list in viewmodel to checkboxes

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Unless your Dictionary has simple value types for both the Key and Value (e.g. public Dictionary<string, string>), the DefaultModelBinder requires that the form control name attributes be in the format

<input .... name="Matrix[0].Key" value="..." />
<input .... name="Matrix[0].Value[0].ID" value="..." />
<input .... name="Matrix[0].Value[0].Name" value="..." />

There are no HtmlHelper methods that will generate the correct html to allow binding to your Dictionary.

It is far simpler to create simple view model(s) to with IList<T> properties for the collections. Based on the view you have shown, those models would be

public class EditVM
{
    public int FooID { get; set; }
    public List<BarVM> Bars { get; set; }
}
public class BarVM
{
    public string Name { get; set; }
    public List<BarVersionVM> Versions { get; set; }
}
public class BarVersionVM
{
    public int ID { get; set; }
    public string Name { get; set; } // not clear where you use this property
    public string Version { get; set; }
    public bool IsSupported { get; set; }
}

and your view would then be

@model EditVM
....
@Html.HiddenFor(m => m.FooID)
@for(int i = 0; i < Model.Bars.Count; i++)
{
    <fieldset>
        <legend>@Model.Bars[i].Name</legend>
        @Html.HiddenFor(m => m.Bars[i].Name) // in case you need to return the view in the POST method
        @for(int j = 0; j < Model.Bars[i].Versions.Count; j++)
        {
            <div>
                @Html.HiddenFor(m => m.Bars[i].Versions[j].ID)
                @Html.CheckBoxFor(m => m.Bars[i].Versions[j].IsSupported)
                @Html.LabelFor((m => m.Bars[i].Versions[j].IsSupported, Model.Bars[i].Versions[j].Version)
            </div>
        }
    </fieldset>
}
<input type="submit" value="Save" />

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