Hey, thanks for the detailed report. The pstack and strace analysis is really helpful.
This is a known regression in the 2026.04.13-a9d7fb5 CLI agent. Another user hit the same issue here: Regression - cpu spikes to 100% and agent hangs
The team is aware of it. Your notes about isolating .git as the trigger, plus the stack traces through merkle-tree-napi, add valuable context for debugging. I’ve passed this along.
As a workaround, if you still have the previous version 2026.03.20-7da3412, you can roll back to it until a fix is out.
Let me know if you have any questions.