I have been using Claude Code on a medium codebase (~2000 files, ~1M lines of code) for over a year and have never had to wait this long. Also I'm on the max plan and have not seen these limits at all.
Just yesterday it thought for 591 seconds for me, which is ten minutes. There have been times this week when it ran longer and I assumed it was just bust and stopped it
Just chipping in to say that I've never seen it churn for more than 20 minutes in two years worth of usage. The longest I've ever seen it churn is when I had it give extremely detailed analysis of five fictional novels simultaneously.