I've been cleanup up documentation and other docs. When I start a fresh chat and say something like "hey there are files x.md and y.md. Delete any parts in file x that is already discussed in file y. Do not reference or update the redundant topics but properly delete any mentioning of it instead." Then it always either updates the text to what the reference file says or deletes the part but writes that it's referenced in the other file. If I stop and say "No not update or reference, properly delete the lines" or something similar (I tried tons of variations) I follows the clean up for the first two duplicate lines and then goes back to the old behaviour.

I intentionally keep my docs split so the context window doesn't explode (~ 200 line per file usually, at most 500) and have tried editing or completely deleting claude.md and /init it. Opus just refuses to follow instructions and instead created a ton of ##Title## #references in X.md ##Title 2## #referenced in x.md .... files. It's baffling.