Split Modification class functionality

This had the potential to cause a lot of issues the way it was. Moving the actual functionality for cleaning, filtering, and applying extras to their appropriate classes allows for less redirection when calling into the code. Modification as a class was essentially a shell around things that should have just been a single call.

SabreTools.Filtering/ExtraIni.cs

@@ -1,6 +1,10 @@
-using System.Collections.Generic;
+using System;
+using System.Collections.Generic;
 
+using SabreTools.Core;
 using SabreTools.Core.Tools;
+using SabreTools.DatFiles;
+using SabreTools.DatItems;
 using SabreTools.Logging;
 
 namespace SabreTools.Filtering
@@ -37,7 +41,7 @@ namespace SabreTools.Filtering
 
         #endregion
 
-        #region Extras Population
+        #region Population
 
         /// <summary>
         /// Populate item using field:file inputs
@@ -68,5 +72,96 @@ namespace SabreTools.Filtering
         }
 
         #endregion
+    
+        #region Running
+
+        /// <summary>
+        /// Apply a set of Extra INIs on the DatFile
+        /// </summary>
+        /// <param name="datFile">Current DatFile object to run operations on</param>
+        /// <param name="throwOnError">True if the error that is thrown should be thrown back to the caller, false otherwise</param>
+        /// <returns>True if the extras were applied, false on error</returns>
+        public bool ApplyExtras(DatFile datFile, bool throwOnError = false)
+        {
+            try
+            {
+                // Bucket by game first
+                datFile.Items.BucketBy(ItemKey.Machine, DedupeType.None);
+
+                // Create a new set of mappings based on the items
+                var machineMap = new Dictionary<string, Dictionary<MachineField, string>>();
+                var datItemMap = new Dictionary<string, Dictionary<DatItemField, string>>();
+
+                // Loop through each of the extras
+                foreach (ExtraIniItem item in Items)
+                {
+                    foreach (var mapping in item.Mappings)
+                    {
+                        string key = mapping.Key;
+                        List<string> machineNames = mapping.Value;
+
+                        // Loop through the machines and add the new mappings
+                        foreach (string machine in machineNames)
+                        {
+                            if (item.MachineField != MachineField.NULL)
+                            {
+                                if (!machineMap.ContainsKey(machine))
+                                    machineMap[machine] = new Dictionary<MachineField, string>();
+
+                                machineMap[machine][item.MachineField] = key;
+                            }
+                            else if (item.DatItemField != DatItemField.NULL)
+                            {
+                                if (!datItemMap.ContainsKey(machine))
+                                    datItemMap[machine] = new Dictionary<DatItemField, string>();
+
+                                datItemMap[machine][item.DatItemField] = key;
+                            }
+                        }
+                    }
+                }
+
+                // Now apply the new set of Machine mappings
+                foreach (string key in machineMap.Keys)
+                {
+                    // If the key doesn't exist, continue
+                    if (!datFile.Items.ContainsKey(key))
+                        continue;
+
+                    List<DatItem> datItems = datFile.Items[key];
+                    var mappings = machineMap[key];
+
+                    foreach (var datItem in datItems)
+                    {
+                        DatItemTool.SetFields(datItem.Machine, mappings);
+                    }
+                }
+
+                // Now apply the new set of DatItem mappings
+                foreach (string key in datItemMap.Keys)
+                {
+                    // If the key doesn't exist, continue
+                    if (!datFile.Items.ContainsKey(key))
+                        continue;
+
+                    List<DatItem> datItems = datFile.Items[key];
+                    var mappings = datItemMap[key];
+
+                    foreach (var datItem in datItems)
+                    {
+                        DatItemTool.SetFields(datItem, mappings, null);
+                    }
+                }
+            }
+            catch (Exception ex) when (!throwOnError)
+            {
+                logger.Error(ex);
+                return false;
+            }
+
+            return true;
+        }
+
+        #endregion
     }
 }