Something seems wrong. A half-million tokens is almost five times larger than I allow even long-running conversations to get too. I've manually disabled the 1M context, so my limit is 200K, and I don't like it to get above 50%.

Is it... not aware of its current directory? Is its current directory not the root of your repo? Have you maybe disabled all tool use? I don't even know how I could get it to do what you're describing.

Maybe spend more time in /plan mode, so it uses tools and the Explore sub-agent to see what the current state of things is?