dotnet-transform-xdt
Global tool for .NET Core 2.1 and later 
.NET Core 2.1 introduces the concept of global tools, meaning that you can install dotnet-xdt using the .NET CLI and use it everywhere. One advantage of this approach is that you can use the same command, for both installation and usage, across all platforms.
⚠️ To use global tools, .Net Core SDK 2.1.300 or later is required.
Install dotnet-xdt as a global tool (only once):
dotnet tool install --global dotnet-xdt --version 2.2.1And then you can apply XDT transforms, from the command-line, anywhere on your PC, e.g.:
dotnet xdt --source original.xml --transform delta.xml --output final.xmlGlobal tools are not ideal when an application needs to build completely self-contained, without relying on tools installed in the surrounding environment. They are also only available on the latest .NET Core.
Read on if this is a concern for your application.
FatAntelope
A tool for comparing .NET .config files and generating a config transform (Microsoft Xml Document Transform).
FatAntelope parses the two config (xml) files into two trees and performs an unordered diff / comparison to identify nodes that have been updated, inserted or deleted, and then generates a XDT transform from these differences.
The XML diff / comparison algorithm is a C# port of the 'XDiff' algorithm described here: http://pages.cs.wisc.edu/~yuanwang/xdiff.html
Try It
A demonstration is setup here: fatantelopetester.apphb.com