Replace Unity sprite packing with custom atlas.

BakeSpriteAtlas.cs

using UnityEngine;
using UnityEditor;
using System.Collections.Generic;
using System.IO;

public class BakeSpriteAtlas : EditorWindow
{
	const string TITLE = "Bake Sprite Atlas";

	[MenuItem ("Window/" + TITLE)]
	static void showWindow ()
	{
		EditorWindow.GetWindow<BakeSpriteAtlas> (TITLE);
	}

	string tagName;
	Texture2D[] textureArray;
	Vector4[] borderArray;
	bool hasBorder;
	Vector2 scrollPosition;
	Texture2D replaceAtlas;
	string replaceFolder = "GameContent";

	void OnGUI ()
	{
		this.tagName = EditorGUILayout.TextField ("Tag", this.tagName);

		if (GUILayout.Button ("1. Search"))
		{
			var guids = AssetDatabase.FindAssets ("t:sprite");
			var assetPathSet = new HashSet<string> ();
			var textureList = new List<Texture2D> ();
			var borderList = new List<Vector4> ();
			this.hasBorder = false;
			for (int i = 0; i < guids.Length; ++i)
			{
				var path = AssetDatabase.GUIDToAssetPath (guids[i]);
				if (assetPathSet.Contains (path))
					continue;
				var importer = AssetImporter.GetAtPath (path) as TextureImporter;
				if (importer == null)
					continue;
				if (importer.spritePackingTag != this.tagName)
					continue;
				textureList.Add (AssetDatabase.LoadAssetAtPath<Texture2D> (path));
				borderList.Add (importer.spriteBorder);
				if (importer.spriteBorder != Vector4.zero)
					this.hasBorder = true;
			}
			this.textureArray = textureList.ToArray ();
			this.borderArray = borderList.ToArray ();
		}

		if (this.textureArray != null && this.borderArray != null)
		{
			this.scrollPosition = EditorGUILayout.BeginScrollView (this.scrollPosition);
			var oriColor = GUI.color;
			for (int i = 0; i < this.textureArray.Length; ++i)
			{
				GUI.color = this.borderArray[i] == Vector4.zero ? oriColor : Color.yellow;
				EditorGUILayout.ObjectField (this.textureArray[i], typeof (Texture2D), false);
			}
			GUI.color = oriColor;
			EditorGUILayout.EndScrollView ();
			if (this.hasBorder)
				EditorGUILayout.LabelField ("* Yellow means it has border settings");
		}

		if (GUILayout.Button ("2. Output (for custom texture packing)"))
		{
			this.output ();
		}

		this.replaceAtlas = (Texture2D) EditorGUILayout.ObjectField (
			"Replace Atlas", this.replaceAtlas, typeof (Texture2D), false);
		this.replaceFolder = EditorGUILayout.TextField ("Replace Folder", this.replaceFolder);

		if (GUILayout.Button ("3. Replace (and delete all original texures)"))
		{
			this.replace ();
		}
	}

	void output ()
	{
		var nameSet = new HashSet<string> ();
		for (int i = 0; i < this.textureArray.Length; ++i)
		{
			var name = this.textureArray[i].name;
			if (nameSet.Contains (name))
			{
				EditorUtility.DisplayDialog ("Output altas texture error", "Find duplicate name: " + name, "OK");
				return;
			}
			nameSet.Add (name);
		}

		var dir = EditorUtility.SaveFolderPanel ("Select output directory", "", "");
		for (int i = 0; i < this.textureArray.Length; ++i)
		{
			var texture = this.textureArray[i];
			var srcPath = AssetDatabase.GetAssetPath (texture);
			File.Copy (srcPath, Path.Combine (dir, Path.GetFileName (srcPath)), true);
		}
	}

	void replace ()
	{
		var replaceAtlasPath = AssetDatabase.GetAssetPath (this.replaceAtlas);
		{
			var name2border = new Dictionary<string, Vector4> ();
			for (int i = 0; i < this.textureArray.Length; ++i)
			{
				if (this.borderArray[i] != Vector4.zero)
				{
					name2border.Add (this.textureArray[i].name, this.borderArray[i]);
				}
			}

			var replaceAtlasImporter = (TextureImporter) AssetImporter.GetAtPath (replaceAtlasPath);
			var spritesheet = replaceAtlasImporter.spritesheet;
			bool dirty = false;
			for (int i = 0; i < spritesheet.Length; ++i)
			{
				Vector4 border;
				if (name2border.TryGetValue (spritesheet[i].name, out border))
				{
					if (spritesheet[i].border != border)
					{
						spritesheet[i].border = border;
						dirty = true;
					}
				}
			}
			if (dirty)
			{
				replaceAtlasImporter.spritesheet = spritesheet;
				EditorUtility.SetDirty (replaceAtlasImporter);
				replaceAtlasImporter.SaveAndReimport ();
				Debug.Log ("Copy border settings automatically.");
			}
		}

		var replaceAtlasGuid = AssetDatabase.AssetPathToGUID (replaceAtlasPath);
		var replaceAtlasMetaLines = File.ReadAllLines (replaceAtlasPath + ".meta");
		var name2fileID = new Dictionary<string, string> ();
		{
			int i = 0;
			for (; i < replaceAtlasMetaLines.Length; ++i)
			{
				var l = replaceAtlasMetaLines[i];
				if (l.EndsWith ("fileIDToRecycleName:"))
				{
					++i;
					break;
				}
			}

			int indent = 0;
			string indentString;
			{
				var l = replaceAtlasMetaLines[i];
				while (l[indent] == ' ')
					++indent;
				indentString = new string (' ', indent);
			}
			for (; i < replaceAtlasMetaLines.Length; ++i)
			{
				var l = replaceAtlasMetaLines[i];
				if (!l.StartsWith (indentString))
					break;
				var colonPos = l.IndexOf (':');
				var fileID = l.Substring (indent, colonPos - indent);
				var name = l.Substring (colonPos + 2);
				name2fileID.Add (name, fileID);
			}
		}

		var replaceDict = new Dictionary <string, string> ();
		for (int i = 0; i < this.textureArray.Length; ++i)
		{
			var fileID = name2fileID[this.textureArray[i].name];
			var replaceTarget = string.Format ("fileID: {0}, guid: {1}", fileID, replaceAtlasGuid);
			var path = AssetDatabase.GetAssetPath (this.textureArray[i]);
			replaceDict.Add (AssetDatabase.AssetPathToGUID (path), replaceTarget);
		}

		var filePathList = new List<string> ();
		getAllFilesMatchingPattern ("Assets/" + this.replaceFolder, filePathList, "*.unity");
		getAllFilesMatchingPattern ("Assets/" + this.replaceFolder, filePathList, "*.prefab");

		var logBuilder = new System.Text.StringBuilder ();
		const string searchPattern = "fileID: 21300000, guid: ";
		const int guidLenght = 32;
		int replaceLength = searchPattern.Length + guidLenght;
		foreach (var path in filePathList)
		{
			var text = File.ReadAllText (path);
			System.Text.StringBuilder textBuilder = null;
			for (int i = 0;; i += replaceLength)
			{
				i = text.IndexOf (searchPattern, i);
				if (i == -1)
					break;
				var guid = text.Substring (i + searchPattern.Length, guidLenght);
				string replaceTarget;
				if (replaceDict.TryGetValue (guid, out replaceTarget))
				{
					if (textBuilder == null)
						textBuilder = new System.Text.StringBuilder (text);
					textBuilder.Remove (i, replaceLength);
					textBuilder.Insert (i, replaceTarget);
				}
			}
			if (textBuilder != null)
			{
				File.WriteAllText (path, textBuilder.ToString ());
				logBuilder.AppendLine (path);
			}
		}

		for (int i = 0; i < this.textureArray.Length; ++i)
		{
			AssetDatabase.DeleteAsset (AssetDatabase.GetAssetPath (this.textureArray[i]));
		}
		this.tagName = null;
		this.textureArray = null;
		this.borderArray = null;
		this.replaceAtlas = null;

		Debug.Log (logBuilder.ToString ());
	}

	static void getAllFilesMatchingPattern (string dir, List<string> filePathList, string searchPattern)
	{
		var files = Directory.GetFiles (dir, searchPattern);
		filePathList.AddRange (files);
		var dirs = Directory.GetDirectories (dir);
		for (int i = 0; i < dirs.Length; ++i)
		{
			getAllFilesMatchingPattern (dirs[i], filePathList, searchPattern);
		}
	}
}