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

1 files changed, 1 insertions, 4 deletions

diff --git a/src/main/claude/index.ts b/src/main/claude/index.ts
index 34a914e..8bdcccd 100644
--- a/src/main/claude/index.ts
+++ b/src/main/claude/index.ts
@@ -45,10 +45,7 @@ export async function sendMessage({
       resume: session.claude_session_id ?? undefined,
       tools: phaseConfig.tools,
       permissionMode: phaseConfig.permissionMode,
-      // Add system prompt via extraArgs since there's no direct option
-      extraArgs: {
-        "system-prompt": phaseConfig.systemPrompt,
-      },
+      systemPrompt: phaseConfig.systemPrompt,
     },
   });