diff --git a/IPA.Injector/IPA.Injector.csproj b/IPA.Injector/IPA.Injector.csproj
index f07fc0af..e8e044a1 100644
--- a/IPA.Injector/IPA.Injector.csproj
+++ b/IPA.Injector/IPA.Injector.csproj
@@ -31,12 +31,6 @@
     <WarningLevel>4</WarningLevel>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="Ionic.Zip, Version=1.9.1.8, Culture=neutral, PublicKeyToken=edbe51ad942a3f5c, processorArchitecture=MSIL">
-      <HintPath>..\packages\Ionic.Zip.1.9.1.8\lib\Ionic.Zip.dll</HintPath>
-    </Reference>
-    <Reference Include="Newtonsoft.Json, Version=11.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
-      <HintPath>..\packages\Newtonsoft.Json.11.0.2\lib\net45\Newtonsoft.Json.dll</HintPath>
-    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -63,9 +57,6 @@
       <Name>IPA.Loader</Name>
     </ProjectReference>
   </ItemGroup>
-  <ItemGroup>
-    <None Include="packages.config" />
-  </ItemGroup>
   <ItemGroup>
     <Content Include="..\Libs\0Harmony.dll">
       <Link>Libraries\Included\0Harmony.dll</Link>
diff --git a/IPA.Injector/packages.config b/IPA.Injector/packages.config
deleted file mode 100644
index 71c37d6d..00000000
--- a/IPA.Injector/packages.config
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<packages>
-  <package id="Ionic.Zip" version="1.9.1.8" targetFramework="net46" />
-  <package id="Newtonsoft.Json" version="11.0.2" targetFramework="net46" />
-</packages>
\ No newline at end of file
diff --git a/IPA.Loader/IPA.Loader.csproj b/IPA.Loader/IPA.Loader.csproj
index fe8d387f..af6be3af 100644
--- a/IPA.Loader/IPA.Loader.csproj
+++ b/IPA.Loader/IPA.Loader.csproj
@@ -33,12 +33,6 @@
     <AllowUnsafeBlocks>true</AllowUnsafeBlocks>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="Ionic.Zip, Version=1.9.1.8, Culture=neutral, PublicKeyToken=edbe51ad942a3f5c, processorArchitecture=MSIL">
-      <HintPath>..\packages\Ionic.Zip.1.9.1.8\lib\Ionic.Zip.dll</HintPath>
-    </Reference>
-    <Reference Include="Newtonsoft.Json, Version=11.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
-      <HintPath>..\packages\Newtonsoft.Json.11.0.2\lib\net45\Newtonsoft.Json.dll</HintPath>
-    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -88,7 +82,15 @@
     <Compile Include="Utilities\SteamCheck.cs" />
   </ItemGroup>
   <ItemGroup>
-    <None Include="packages.config" />
+    <PackageReference Include="Ionic.Zip">
+      <Version>1.9.1.8</Version>
+    </PackageReference>
+    <PackageReference Include="Mono.Cecil">
+      <Version>0.9.6.4</Version>
+    </PackageReference>
+    <PackageReference Include="Newtonsoft.Json">
+      <Version>11.0.2</Version>
+    </PackageReference>
   </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
 </Project>
\ No newline at end of file
diff --git a/IPA.Loader/packages.config b/IPA.Loader/packages.config
deleted file mode 100644
index 71c37d6d..00000000
--- a/IPA.Loader/packages.config
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<packages>
-  <package id="Ionic.Zip" version="1.9.1.8" targetFramework="net46" />
-  <package id="Newtonsoft.Json" version="11.0.2" targetFramework="net46" />
-</packages>
\ No newline at end of file
diff --git a/IPA/IPA.csproj b/IPA/IPA.csproj
index 1bb17d89..705e0703 100644
--- a/IPA/IPA.csproj
+++ b/IPA/IPA.csproj
@@ -13,6 +13,21 @@
     <FileAlignment>512</FileAlignment>
     <TargetFrameworkProfile>
     </TargetFrameworkProfile>
+    <PublishUrl>publish\</PublishUrl>
+    <Install>true</Install>
+    <InstallFrom>Disk</InstallFrom>
+    <UpdateEnabled>false</UpdateEnabled>
+    <UpdateMode>Foreground</UpdateMode>
+    <UpdateInterval>7</UpdateInterval>
+    <UpdateIntervalUnits>Days</UpdateIntervalUnits>
+    <UpdatePeriodically>false</UpdatePeriodically>
+    <UpdateRequired>false</UpdateRequired>
+    <MapFileExtensions>true</MapFileExtensions>
+    <ApplicationRevision>0</ApplicationRevision>
+    <ApplicationVersion>1.0.0.%2a</ApplicationVersion>
+    <IsWebBootstrapper>false</IsWebBootstrapper>
+    <UseApplicationTrust>false</UseApplicationTrust>
+    <BootstrapperEnabled>true</BootstrapperEnabled>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
     <PlatformTarget>AnyCPU</PlatformTarget>
@@ -39,23 +54,10 @@
   <PropertyGroup>
     <ApplicationIcon>favicon.ico</ApplicationIcon>
   </PropertyGroup>
+  <PropertyGroup>
+    <StartupObject>IPA.Program</StartupObject>
+  </PropertyGroup>
   <ItemGroup>
-    <Reference Include="Mono.Cecil, Version=0.9.6.0, Culture=neutral, PublicKeyToken=0738eb9f132ed756, processorArchitecture=MSIL">
-      <HintPath>..\packages\Mono.Cecil.0.9.6.4\lib\net45\Mono.Cecil.dll</HintPath>
-      <Private>True</Private>
-    </Reference>
-    <Reference Include="Mono.Cecil.Mdb, Version=0.9.6.0, Culture=neutral, PublicKeyToken=0738eb9f132ed756, processorArchitecture=MSIL">
-      <HintPath>..\packages\Mono.Cecil.0.9.6.4\lib\net45\Mono.Cecil.Mdb.dll</HintPath>
-      <Private>False</Private>
-    </Reference>
-    <Reference Include="Mono.Cecil.Pdb, Version=0.9.6.0, Culture=neutral, PublicKeyToken=0738eb9f132ed756, processorArchitecture=MSIL">
-      <HintPath>..\packages\Mono.Cecil.0.9.6.4\lib\net45\Mono.Cecil.Pdb.dll</HintPath>
-      <Private>False</Private>
-    </Reference>
-    <Reference Include="Mono.Cecil.Rocks, Version=0.9.6.0, Culture=neutral, PublicKeyToken=0738eb9f132ed756, processorArchitecture=MSIL">
-      <HintPath>..\packages\Mono.Cecil.0.9.6.4\lib\net45\Mono.Cecil.Rocks.dll</HintPath>
-      <Private>False</Private>
-    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Windows.Forms" />
@@ -77,7 +79,6 @@
   </ItemGroup>
   <ItemGroup>
     <None Include="app.config" />
-    <None Include="packages.config" />
   </ItemGroup>
   <ItemGroup>
     <Content Include="favicon.ico" />
@@ -85,6 +86,23 @@
   <ItemGroup>
     <Folder Include="IPA\Fallback\" />
   </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="Mono.Cecil">
+      <Version>0.9.6.4</Version>
+    </PackageReference>
+  </ItemGroup>
+  <ItemGroup>
+    <BootstrapperPackage Include=".NETFramework,Version=v4.6.2">
+      <Visible>False</Visible>
+      <ProductName>Microsoft .NET Framework 4.6.2 %28x86 and x64%29</ProductName>
+      <Install>true</Install>
+    </BootstrapperPackage>
+    <BootstrapperPackage Include="Microsoft.Net.Framework.3.5.SP1">
+      <Visible>False</Visible>
+      <ProductName>.NET Framework 3.5 SP1</ProductName>
+      <Install>false</Install>
+    </BootstrapperPackage>
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.
diff --git a/IPA/PatchContext.cs b/IPA/PatchContext.cs
index 81ec755c..8d72ebf1 100644
--- a/IPA/PatchContext.cs
+++ b/IPA/PatchContext.cs
@@ -38,7 +38,7 @@ namespace IPA
                 Executable = exe
             };
             context.ProjectRoot = new FileInfo(context.Executable).Directory.FullName;
-            context.IPARoot = Path.Combine(context.ProjectRoot, "IPA");
+            context.IPARoot = Path.Combine(Path.GetDirectoryName(Assembly.GetEntryAssembly().Location), "IPA");
             context.IPA = Assembly.GetExecutingAssembly().Location ?? Path.Combine(context.ProjectRoot, "IPA.exe");
             context.DataPathSrc = Path.Combine(context.IPARoot, "Data");
             context.LibsPathSrc = Path.Combine(context.IPARoot, "Libs");
diff --git a/IPA/Patcher/BackupManager.cs b/IPA/Patcher/BackupManager.cs
index c129c397..08ee47d1 100644
--- a/IPA/Patcher/BackupManager.cs
+++ b/IPA/Patcher/BackupManager.cs
@@ -30,10 +30,40 @@ namespace IPA.Patcher
             {
                 backup.Restore();
                 backup.Delete();
+                DeleteEmptyDirs(context.ProjectRoot);
                 return true;
             }
             return false;
         }
 
+        public static void DeleteEmptyDirs(string dir)
+        {
+            if (string.IsNullOrEmpty(dir))
+                throw new ArgumentException(
+                    "Starting directory is a null reference or an empty string",
+                    "dir");
+
+            try
+            {
+                foreach (var d in Directory.EnumerateDirectories(dir))
+                {
+                    DeleteEmptyDirs(d);
+                }
+
+                var entries = Directory.EnumerateFileSystemEntries(dir);
+
+                if (!entries.Any())
+                {
+                    try
+                    {
+                        Directory.Delete(dir);
+                    }
+                    catch (UnauthorizedAccessException) { }
+                    catch (DirectoryNotFoundException) { }
+                }
+            }
+            catch (UnauthorizedAccessException) { }
+        }
+
     }
 }
diff --git a/IPA/Patcher/BackupUnit.cs b/IPA/Patcher/BackupUnit.cs
index 22763338..0656db52 100644
--- a/IPA/Patcher/BackupUnit.cs
+++ b/IPA/Patcher/BackupUnit.cs
@@ -13,11 +13,12 @@ namespace IPA.Patcher
     public class BackupUnit
     {
         public string Name { get; private set; }
-
+        
         private DirectoryInfo _BackupPath;
         private PatchContext _Context;
         private List<string> _Files = new List<string>();
-
+        private FileInfo _ManifestFile;
+        private static string _ManifestFileName = "$manifest$.txt";
 
 
         public BackupUnit(PatchContext context) : this(context, DateTime.Now.ToString("yyyy-MM-dd_h-mm-ss"))
@@ -29,16 +30,28 @@ namespace IPA.Patcher
             Name = name;
             _Context = context;
             _BackupPath = new DirectoryInfo(Path.Combine(_Context.BackupPath, Name));
+            _ManifestFile = new FileInfo(Path.Combine(_BackupPath.FullName, _ManifestFileName));
         }
         
         public static BackupUnit FromDirectory(DirectoryInfo directory, PatchContext context)
         {
             var unit = new BackupUnit(context, directory.Name);
 
-            // Parse directory
-            foreach(var file in directory.GetFiles("*", SearchOption.AllDirectories)) {
-                var relativePath = file.FullName.Substring(directory.FullName.Length + 1);
-                unit._Files.Add(relativePath);
+            // Read Manifest
+            if (unit._ManifestFile.Exists)
+            {
+                string manifest = File.ReadAllText(unit._ManifestFile.FullName);
+                foreach (var line in manifest.Split(new string[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries))
+                    unit._Files.Add(line);
+            }
+            else
+            {
+                foreach (var file in directory.GetFiles("*", SearchOption.AllDirectories))
+                {
+                    if (file.Name == _ManifestFileName) continue;
+                    var relativePath = file.FullName.Substring(directory.FullName.Length + 1);
+                    unit._Files.Add(relativePath);
+                }
             }
 
             return unit;
@@ -74,19 +87,25 @@ namespace IPA.Patcher
                 Console.WriteLine("Skipping backup of {0}", relativePath);
                 return;
             }
-
-
+            
             // Copy over
             backupPath.Directory.Create();
             if (file.Exists)
             {
                 file.CopyTo(backupPath.FullName);
-            } else
+            }
+            else
             {
                 // Make empty file
                 backupPath.Create().Close();
             }
 
+            if (!File.Exists(_ManifestFile.FullName))
+                _ManifestFile.Create().Close();
+            var stream = _ManifestFile.AppendText();
+            stream.WriteLine(relativePath);
+            stream.Close();
+
             // Add to list
             _Files.Add(relativePath);
         }
diff --git a/IPA/Program.cs b/IPA/Program.cs
index e697345d..57924fe7 100644
--- a/IPA/Program.cs
+++ b/IPA/Program.cs
@@ -32,7 +32,7 @@ namespace IPA {
         static void Main(string[] args)
         {
             Arguments.CmdLine.Flags(ArgHelp, ArgWaitFor, ArgForce, ArgRevert, ArgNoWait, ArgStart, ArgLaunch).Process();
-
+           
             if (ArgHelp)
             {
                 Arguments.CmdLine.PrintHelp();
@@ -351,7 +351,7 @@ namespace IPA {
 
 
         static void Fail(string message) {
-            Console.Error.Write("ERROR: " + message);
+            Console.Error.WriteLine("ERROR: " + message);
 
             WaitForEnd();
 
diff --git a/IPA/obj/Debug/IPA.csproj.CoreCompileInputs.cache b/IPA/obj/Debug/IPA.csproj.CoreCompileInputs.cache
index d0c0594d..7a5f217b 100644
--- a/IPA/obj/Debug/IPA.csproj.CoreCompileInputs.cache
+++ b/IPA/obj/Debug/IPA.csproj.CoreCompileInputs.cache
@@ -1 +1 @@
-854dcf24535098612cfeca06e87fe2b163332578
+1d38dd5b9139545c6bc300c735ca121563a74d20
diff --git a/IPA/packages.config b/IPA/packages.config
deleted file mode 100644
index f30e7947..00000000
--- a/IPA/packages.config
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<packages>
-  <package id="Mono.Cecil" version="0.9.6.4" targetFramework="net462" />
-</packages>
\ No newline at end of file