Leave them where they are. You may want to read and perhaps modify them.
These are the way AI remembers goal, context, and history of what it’s doing on your site. Essentially, the plan and the result from previous sessions.
From time to time I go back and read those .md files the AI is using and verify that what’s in them that implies how the AI should work is exactly what I want. I sometimes add to the backlog.md file. I often update the style files. When I do that, I’ll preface my next session with a prompt that says “I’ve updated the .md files [or specific file] you’re keeping to better reflect what we’re trying to do…” even though the AI should pick that up on its own. Sometimes—I’m using Claude, not all AI will do this—that will prompt some questions from the AI about the change(s).
Hmmm, they shouldn’t be editable, are you editing them in Elements? 
Yes. I’m doing MCP. I have Claude keep copies where I can get to them.
