DepthFirstSearch.cs

void Main()
{
    var hoge = new[]
    {
        "ccc/hoge/Resources/fuga/tyger",
        "ghoge/Resources/fuga/tyger",
        "zxvzxvcz/Resources/fuga/tyger/hogemoge",
        "test/fuga/Resources/fuga/tyger",
        "asdfadga/fuga/Resources/fuga/tyger/hogemoge",
    };

    var concat = hoge.OrderBy(x => x).Select(x =>
    {
        var index = x.LastIndexOf("Resources", System.StringComparison.InvariantCultureIgnoreCase);
        var name = x.Substring(index, x.Length - index).Replace("Resources/", "").Replace("resources/", "");
        return new ResourceInfo(x, name);
    })
    .ToArray();

    var duplicates = concat.GroupBy(x => x.Name).Where(x => x.Count() > 1).ToArray();
    if (duplicates.Any())
    {
        var dup = duplicates.SelectMany(x => x.OrderBy(y => y.SubdirectoryCount).Skip(1));
        concat.Except(dup).Dump();
    }

}

// Define other methods and classes here

private struct ResourceInfo
{
    public string Path;
    public string Name;
    public int SubdirectoryCount;

    public ResourceInfo(string path, string name)
    {
        Path = path;
        Name = name;
        SubdirectoryCount = Path.Replace("/" + Name, "").Count(y => y == '/');
    }
}