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src/FileSearchCriteria.cs

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+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+
+namespace ProjectNugetDuplicateFinder
+{
+    public class FileSearchCriteria
+    {
+        public string[] Extensions { get; set; } = new string[0];
+
+        public string BaseDirectory { get; set; }
+
+        public string[] TargetDirectories { get; set; } = new string[0];
+
+        public IEnumerable<string> AbsoluteTargetDirectories
+        {
+            get
+            {
+                return TargetDirectories?
+                    .Select(td => Path.Combine(BaseDirectory, td))
+                    .Where(td => !string.IsNullOrWhiteSpace(td) && Directory.Exists(td));
+            }
+        }
+
+        public bool Recursive { get; set; }
+
+        public SearchOption SearchOption
+        {
+            get
+            {
+                return Recursive ? SearchOption.AllDirectories : SearchOption.TopDirectoryOnly;
+            }
+        }
+
+    }
+}

src/Program.cs

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+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Xml.Linq;
+using Semver;
+
+namespace ProjectNugetDuplicateFinder
+{
+    class Program
+    {
+        static void Main(string[] args)
+        {
+            var searchCriteria = new FileSearchCriteria
+            {
+                Extensions = new string[] { ".csproj" },
+                BaseDirectory = "D:\\Projects\\onelia",
+                TargetDirectories = new string[] { "onelia" },
+                Recursive = true,
+            };
+
+            var result = new Finder().Find(searchCriteria);
+
+
+            //result = result.Where(f => f.EndsWith("Falcon.Api.Payment.Tests.csproj")).ToList();
+
+            foreach (var project in result)
+            {
+                try
+                {
+                    var text = File.ReadAllText(project);
+                    var document = XDocument.Parse(text);
+                    var dublicates = document
+                        .Descendants("ItemGroup")
+                        .Descendants("PackageReference")
+                        .GroupBy(f => f.Attribute("Include").Value.ToLower())
+                        .Where(f => f.Count() > 1);
+
+                    var isAnyRemoved = false;
+                    foreach (var duplicate in dublicates)
+                    {
+                        var maxVersion = duplicate.Max(f => SemVersion.Parse(f.Attribute("Version").Value));
+
+                        var max = duplicate.First(f => f.Attribute("Version").Value == maxVersion.ToString());
+                        IEnumerable<XElement> toRemove = duplicate.Except(new List<XElement> { max });
+                        foreach (var xElement in toRemove)
+                        {
+                            xElement.Remove();
+                            isAnyRemoved = true;
+                        }
+                    }
+
+                    if (isAnyRemoved)
+                    {
+                        var newXml = document.ToString();
+                        File.WriteAllText(project, newXml);
+                    }
+                }
+                catch (Exception ex)
+                {
+                    Console.WriteLine(ex);
+                }
+            }
+
+            Console.WriteLine(string.Join("\n", result));
+            Console.ReadLine();
+        }
+    }
+}

src/ProjectGinder.cs

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+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Text;
+
+namespace ProjectNugetDuplicateFinder
+{
+    public class Finder
+    {
+        public IEnumerable<string> Find(FileSearchCriteria criteria)
+        {
+            return criteria.AbsoluteTargetDirectories.SelectMany(td => FindFiles(td, criteria.Extensions, criteria.SearchOption));
+        }
+
+        public IEnumerable<string> FindFiles(string folderPath, string[] extensions, SearchOption searchOption)
+        {
+            return Directory.GetFiles(folderPath, "*.*", searchOption)
+                .Where(s =>
+                    !extensions.Any() ||
+                    extensions.Any(e => string.Compare(e, Path.GetExtension(s), true) == 0)
+                );
+        }
+    }
+}

src/ProjectNugetDuplicateFinder.csproj

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+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>netcoreapp3.1</TargetFramework>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="semver" Version="2.0.6" />
+  </ItemGroup>
+
+</Project>