Clean Unity project from empty folders

RemoveEmptyFolders.cs

using System.IO;
using System.Linq;
using UnityEditor;
using UnityEngine;

public class RemoveEmptyFolders
{
	/// <summary>
	/// Use this flag to simulate a run, before really deleting any folders.
	/// </summary>
	private static bool dryRun = true;
	
	[MenuItem("Tools/Remove empty folders")]
	private static void RemoveEmptyFoldersMenuItem()
	{
		var index = Application.dataPath.IndexOf("/Assets");
		var projectSubfolders = Directory.GetDirectories(Application.dataPath, "*", SearchOption.AllDirectories);

		// Create a list of all the empty subfolders under Assets.
		var emptyFolders = projectSubfolders.Where(path => IsEmptyRecursive(path)).ToArray();
		
		foreach (var folder in emptyFolders)
		{
			// Verify that the folder exists (may have been already removed).
			if (Directory.Exists (folder))
			{
				Debug.Log ("Deleting : " + folder);

				if (!dryRun)
				{
					// Remove dir (recursively)
					Directory.Delete(folder, true);

					// Sync AssetDatabase with the delete operation.
					AssetDatabase.DeleteAsset(folder.Substring(index + 1));
				}
			}
		}

		// Refresh the asset database once we're done.
		AssetDatabase.Refresh();
	}

	/// <summary>
	/// A helper method for determining if a folder is empty or not.
	/// </summary>
	private static bool IsEmptyRecursive(string path)
	{
		// A folder is empty if it (and all its subdirs) have no files (ignore .meta files)
		return Directory.GetFiles(path).Select(file => !file.EndsWith(".meta")).Count() == 0
			&& Directory.GetDirectories(path, string.Empty, SearchOption.AllDirectories).All(IsEmptyRecursive);
	}
}

Thanks for this Gist. Was seeing a some issues in regards to finding the correct folders to remove. The fixed IsEmptyRecursive below:

return Directory.GetFiles(path).Where(file => !file.EndsWith(".meta")).Count() == 0
    && Directory.GetDirectories(path, "*", SearchOption.AllDirectories).All(IsEmptyRecursive);

1. Changed .Select() to .Where() for filtering the files.
2. Changed the empty string filter to wildcard * for retrieving the directories.

Thanks for the input! I extended it for auto deletion, show and remove empty folders.
https://gist.github.com/mrwellmann/c9c6bc416143a58d734077ffe57179a3