Fix: system prompt passing and strengthen phase enforcement

- 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

0 files changed, 0 insertions, 0 deletions