Try this: Keep your CLAUDE.md as simple as possible, disable skills, and request Opus to start a subagent for each of the files and process at most 10 at a time (so you don't get rate limited) and give it the instructions in the skill for whatever processing you're doing to the markdowns as a prompt, see if that helps.

Try the latest skill-creator, has a/b testing

yes we had to tune the claude.md and the skill trigger quite a bit, to get it much better. But to be honest also 4.6 did improve it quite a bit. Did you run into your issues under 4.5 or 4.6?