[BUG] Todo's don't seem to reliably survive compaction

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 0.2.103 (Claude Code)
• Operating System: <!-- e.g. macOS 14.3, Windows 11, Ubuntu 22.04 -->
• Terminal: <!-- e.g. iTerm2, Terminal App -->

Bug Description

I was working on a project with a long (43 task) Todo list. After compaction...the incomplete tasks were just gone. I asked Claude to show me the full todo list and...the incomplete tasks weren't there.

Steps to Reproduce

1. Give Claude a long todo list
2. Fill the context window
3. Notice that tasks are missing

Actual Behavior

Compaction resulted in missing tasks

Additional Context

Todos feel like they really ought to get persisted to disk.