diff --git a/SabreTools.Helper/Tools/ArchiveTools.cs b/SabreTools.Helper/Tools/ArchiveTools.cs
index 06063807..cb29798c 100644
--- a/SabreTools.Helper/Tools/ArchiveTools.cs
+++ b/SabreTools.Helper/Tools/ArchiveTools.cs
@@ -19,31 +19,67 @@ namespace SabreTools.Helper
 		/// <param name="output">Output directory to build to</param>
 		/// <param name="archiveType">Type of archive to attempt to write to</param>
 		/// <param name="rom">RomData representing the new information</param>
-		public static void WriteArchiveOrFile(string input, string output, ArchiveType archiveType, RomData rom)
+		public static void WriteFileToArchive(string input, string output, ArchiveType archiveType, RomData rom)
 		{
 			string archiveFileName = output + Path.DirectorySeparatorChar + rom.Game + ".zip";
 			string singleFileName = output + Path.DirectorySeparatorChar + rom.Game + Path.DirectorySeparatorChar + rom.Name;
 
-			IWriter outarchive = null;
-			FileStream fs = null;
+			IWritableArchive outarchive = null;
 			try
 			{
-				fs = File.OpenWrite(archiveFileName);
-				outarchive = WriterFactory.Open(fs, ArchiveType.Zip, CompressionType.Deflate);
-				outarchive.Write(rom.Name, input);
-			}
-			catch
-			{
-				if (!File.Exists(singleFileName))
+				if (!File.Exists(archiveFileName))
 				{
-					File.Copy(input, singleFileName);
+					outarchive = ArchiveFactory.Create(archiveType) as IWritableArchive;
 				}
+				else
+				{
+					outarchive = ArchiveFactory.Open(archiveFileName, Options.LookForHeader) as IWritableArchive;
+				}
+				outarchive.AddEntry(rom.Name, input);
+				outarchive.SaveTo(archiveFileName, new CompressionInfo { Type = CompressionType.Deflate });
+			}
+			catch (Exception ex)
+			{
+				Console.WriteLine(ex);
+			}
+			finally
+			{
+				outarchive?.Dispose();
+			}
+		}
+
+		/// <summary>
+		/// Copy a file either to an output archive or to an output folder
+		/// </summary>
+		/// <param name="input">Input filename to be moved</param>
+		/// <param name="output">Output directory to build to</param>
+		/// <param name="archiveType">Type of archive to attempt to write to</param>
+		/// <param name="rom">RomData representing the new information</param>
+		public static void WriteFolderToArchive(string input, string output, ArchiveType archiveType)
+		{
+			string archiveFileName = output + Path.DirectorySeparatorChar + Path.GetFileNameWithoutExtension(input) + ".zip";
+
+			IWritableArchive outarchive = null;
+			try
+			{
+				if (!File.Exists(archiveFileName))
+				{
+					outarchive = ArchiveFactory.Create(archiveType) as IWritableArchive;
+				}
+				else
+				{
+					outarchive = ArchiveFactory.Open(archiveFileName, Options.LookForHeader) as IWritableArchive;
+				}
+				outarchive.AddAllFromDirectory(input, "*", SearchOption.AllDirectories);
+				outarchive.SaveTo(archiveFileName, new CompressionInfo { Type = CompressionType.Deflate });
+			}
+			catch (Exception ex)
+			{
+				Console.WriteLine(ex);
 			}
 			finally
 			{
 				outarchive?.Dispose();
-				fs?.Close();
-				fs?.Dispose();
 			}
 		}
 
diff --git a/SabreTools.Helper/Tools/Output.cs b/SabreTools.Helper/Tools/Output.cs
index b0b75899..3e1caf2d 100644
--- a/SabreTools.Helper/Tools/Output.cs
+++ b/SabreTools.Helper/Tools/Output.cs
@@ -608,7 +608,7 @@ namespace SabreTools.Helper
 				long adjustedLength = br.BaseStream.Length - bytesToRemoveFromTail;
 
 				// Seek to the correct position
-				br.BaseStream.Seek(bytesToRemoveFromHead, SeekOrigin.Begin);
+				br.BaseStream.Seek((bytesToRemoveFromHead < 0 ? 0 : bytesToRemoveFromHead), SeekOrigin.Begin);
 
 				// Now read the file in chunks and write out
 				byte[] buffer = new byte[bufferSize];
@@ -695,5 +695,22 @@ namespace SabreTools.Helper
 				}
 			}
 		}
-	}
+
+		/// <summary>
+		/// Copy a file to a new location, creating directories as needed
+		/// </summary>
+		/// <param name="input">Input filename</param>
+		/// <param name="output">Output filename</param>
+		public static void CopyFileToNewLocation(string input, string output)
+		{
+			if (File.Exists(input) && !File.Exists(output))
+			{
+				if (!Directory.Exists(Path.GetDirectoryName(output)))
+				{
+					Directory.CreateDirectory(Path.GetDirectoryName(output));
+				}
+				File.Copy(input, output);
+			}
+		}
+		}
 }
diff --git a/SabreTools.Helper/Tools/RomTools.cs b/SabreTools.Helper/Tools/RomTools.cs
index d59ac89b..dcdd0ae8 100644
--- a/SabreTools.Helper/Tools/RomTools.cs
+++ b/SabreTools.Helper/Tools/RomTools.cs
@@ -16,6 +16,7 @@ namespace SabreTools.Helper
 		/// <param name="noMD5">True if MD5 hashes should not be calculated, false otherwise</param>
 		/// <param name="noSHA1">True if SHA-1 hashes should not be calcluated, false otherwise</param>
 		/// <returns>Populated RomData object if success, empty one on error</returns>
+		/// <remarks>Add read-offset for hash info</remarks>
 		public static RomData GetSingleFileInfo(string input, bool noMD5 = false, bool noSHA1 = false)
 		{
 			RomData rom = new RomData
diff --git a/SimpleSort/SimpleSort.cs b/SimpleSort/SimpleSort.cs
index 3051d02a..c03828e7 100644
--- a/SimpleSort/SimpleSort.cs
+++ b/SimpleSort/SimpleSort.cs
@@ -1,4 +1,5 @@
 using SabreTools.Helper;
+using SharpCompress.Archive;
 using SharpCompress.Common;
 using System;
 using System.Collections.Generic;
@@ -249,6 +250,16 @@ namespace SabreTools
 				_outdir = Path.GetFullPath(_outdir);
 			}
 
+			// Then create or clean the temp directory
+			if (!Directory.Exists(_tempdir))
+			{
+				Directory.CreateDirectory(_tempdir);
+			}
+			else
+			{
+				Output.CleanDirectory(_tempdir);
+			}
+
 			// Then, loop through and check each of the inputs
 			_logger.User("Starting to loop through inputs");
 			foreach (string input in _inputs)
@@ -275,6 +286,20 @@ namespace SabreTools
 				}
 			}
 
+			// Now process the output directory and write all to zipfiles
+			foreach (string dir in Directory.EnumerateDirectories(_outdir, "*", SearchOption.TopDirectoryOnly))
+			{
+				ArchiveTools.WriteFolderToArchive(dir, _outdir, ArchiveType.Zip);
+				try
+				{
+					Directory.Delete(dir, true);
+				}
+				catch (Exception ex)
+				{
+					_logger.Error(ex.ToString());
+				}
+			}
+
 			// Now one final delete of the temp directory
 			Directory.Delete(_tempdir, true);
 
@@ -295,21 +320,93 @@ namespace SabreTools
 			input = Path.GetFullPath(input);
 			_logger.User("Beginning processing of '" + input + "'");
 
-			// Get the hash of the file first
-			RomData rom = RomTools.GetSingleFileInfo(input);
-
-			// If we have a blank RomData, it's an error
-			if (rom.Name == null)
+			// If we have an archive, scan it if necessary
+			bool shouldscan = true;
+			try
 			{
-				return false;
+				IArchive temp = ArchiveFactory.Open(input);
+				switch (temp.Type)
+				{
+					case ArchiveType.GZip:
+						shouldscan = (_gz != ArchiveScanLevel.Internal);
+						break;
+					case ArchiveType.Rar:
+						shouldscan = (_rar != ArchiveScanLevel.Internal);
+						break;
+					case ArchiveType.SevenZip:
+						shouldscan = (_7z != ArchiveScanLevel.Internal);
+						break;
+					case ArchiveType.Zip:
+						shouldscan = (_zip != ArchiveScanLevel.Internal);
+						break;
+				}
+			}
+			catch
+			{
+				shouldscan = true;
 			}
 
-			// Try to find the matches to the file that was found
-			List<RomData> foundroms = RomTools.GetDuplicates(rom, _datdata);
-			_logger.User("File '" + input + "' had " + foundroms.Count + " matches in the DAT!");
-			foreach (RomData found in foundroms)
+			// Hash and match the external files
+			if (shouldscan)
 			{
-				ArchiveTools.WriteArchiveOrFile(input, _outdir, ArchiveType.Zip, found);
+				RomData rom = RomTools.GetSingleFileInfo(input);
+
+				// If we have a blank RomData, it's an error
+				if (rom.Name == null)
+				{
+					return false;
+				}
+
+				// Try to find the matches to the file that was found
+				List<RomData> foundroms = RomTools.GetDuplicates(rom, _datdata);
+				_logger.User("File '" + input + "' had " + foundroms.Count + " matches in the DAT!");
+				foreach (RomData found in foundroms)
+				{
+					_logger.Log("Matched name: " + found.Name);
+					string singleFileName = _outdir + Path.DirectorySeparatorChar + found.Game + Path.DirectorySeparatorChar + found.Name;
+					Output.CopyFileToNewLocation(input, singleFileName);
+				}
+
+				// Now get the headerless file if it exists
+				int hs = 0;
+				RomTools.GetFileHeaderType(input, out hs, _logger);
+				if (hs > 0)
+				{
+					string newinput = input + ".new";
+					_logger.Log("Creating unheadered file: '" + newinput + "'");
+					Output.RemoveBytesFromFile(input, newinput, hs, 0);
+					RomData drom = RomTools.GetSingleFileInfo(newinput);
+
+					// If we have a blank RomData, it's an error
+					if (drom.Name == null)
+					{
+						return false;
+					}
+
+					// Try to find the matches to the file that was found
+					List<RomData> founddroms = RomTools.GetDuplicates(drom, _datdata);
+					_logger.User("File '" + newinput + "' had " + founddroms.Count + " matches in the DAT!");
+					foreach (RomData found in founddroms)
+					{
+						_logger.Log("Matched name: " + found.Name);
+
+						// First output the headerless rom
+						string singleFileName = _outdir + Path.DirectorySeparatorChar + found.Game + Path.DirectorySeparatorChar + found.Name;
+						Output.CopyFileToNewLocation(newinput, singleFileName);
+
+						// Then output the headered rom (renamed)
+						RomData newfound = found;
+						newfound.Name = Path.GetFileNameWithoutExtension(newfound.Name) + " (" + rom.CRC + ")" + Path.GetExtension(newfound.Name);
+
+						_logger.Log("Matched name: " + newfound.Name);
+
+						singleFileName = _outdir + Path.DirectorySeparatorChar + newfound.Game + Path.DirectorySeparatorChar + newfound.Name;
+						Output.CopyFileToNewLocation(input, singleFileName);
+					}
+
+					// Now remove this temporary file
+					File.Delete(newinput);
+				}
 			}
 
 			// Now, if the file is a supported archive type, also run on all files within