ConfigTransformations.cs

using System;
using System.Xml;
using Microsoft.Web.XmlTransform;
using Umbraco.Core.IO;
using Umbraco.Core.Logging;
using umbraco.interfaces;

namespace Our.Umbraco.Packaging
{
    public class ConfigTransformations : IPackageAction
    {
        public string Alias()
        {
            return "configTransformations";
        }

        public bool Execute(string packageName, XmlNode xmlData)
        {
            foreach (XmlNode transConfig in xmlData.SelectNodes("//Transformation"))
            {
                // Get config paths
                var srcFile = IOHelper.MapPath(transConfig.Attributes["src"].Value);
                var targetFile = IOHelper.MapPath(transConfig.Attributes["target"].Value);

                try
                {
                    // Load input file
                    var doc = new XmlDocument();
                    doc.Load(targetFile);

                    // Transform file
                    var trans = new XmlTransformation(srcFile);
                    trans.Apply(doc);

                    // Resave input file
                    doc.Save(targetFile);

                }
                catch (Exception ex)
                {
                    LogHelper.Error<ConfigTransformations>(string.Format("Error applying config transformation {0} to config file {1}",
                        srcFile,
                        targetFile), ex);
                }

            }

            return true;
        }

        public bool Undo(string packageName, XmlNode xmlData)
        {
            return true; // Don't support uninstall
        }

        public XmlNode SampleXml()
        {
            return null;
        }
    }

}

Notes.txt

Make sure to install / reference via Nuget 'Microsoft.Web.Xdt'

Package.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<umbPackage>
  
  <info>
    ...
  </info>
  <Languages />
  <DictionaryItems />
  <Stylesheets />
  <DataTypes />
  <Macros />
  <Templates />
  <DocumentTypes />

  <Actions>
    <Action runat="install" alias="configTransformations">
      <Transformation src="~/App_Plugins/MyPackage/ConfigTransformations/ExamineIndex.config" target="~/config/ExamineIndex.config" />
      <Transformation src="~/App_Plugins/MyPackage/ConfigTransformations/ExamineSettings.config" target="~/config/ExamineSettings.config" />
      <Transformation src="~/App_Plugins/MyPackage/ConfigTransformations/Log4Net.config" target="~/config/log4net.config" />
      <Transformation src="~/App_Plugins/MyPackage/ConfigTransformations/UmbracoSettings.config" target="~/config/umbracoSettings.config" />
      <Transformation src="~/App_Plugins/MyPackage/ConfigTransformations/ViewsWeb.config" target="~/Views/Web.config" />
      <Transformation src="~/App_Plugins/MyPackage/ConfigTransformations/Web.config" target="~/Web.config" />
    </Action>
  </Actions>

  <control />
  <files />
  
</umbPackage>