Updating Internal Links: Removes File Extension When Using Markdown Links

This has actually consequences for interoperability as well and can be confusing to tryage. An example is my feature request Reconsider requirement for markdown links to be urlencoded, wherein I thought at first the problem was that another app (DevonThink in this case) was unable to use urlencoded relative paths only to find out later, that it was actually just the missing extension that caused problems.