I had the exact requirement embedmd was made to solve several months ago and ended up creating my own (
https://github.com/chad-autry/relative-file-inliner if interested). However, after using it briefly I realized I prefer to edit everything directly in the markdwon so I really wanted the reverse. Ended up making
https://github.com/chad-autry/markdown-code-extractor
It extracts code blocks preceded by a relative link a file given by the relative link.