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- Fix systemPrompt option (was incorrectly using extraArgs)
- Rewrite research phase prompt:
- Emphasize writing to research.md as PRIMARY output
- Explicitly forbid asking about phase transitions
- Add document format template
- Clarify that chat is for questions only
- Rewrite plan phase prompt:
- Same emphasis on plan.md as primary output
- Include code snippet format examples
- Forbid implementation attempts
- Change research/plan permissionMode to acceptEdits (was 'plan')
- 'plan' mode may have been blocking file writes
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