Fix: Correct GitHub API instructions for comment responses

Address review feedback: GitHub issue/PR timeline comments don't support
threaded replies. Updated the agent prompt to:

- Remove reference to non-existent /issues/comments/{id}/replies endpoint
- Clarify that issue comments require creating new comments with references
- Keep in_reply_to for PR review comments (which do support threading)
- Update workflow instructions to be consistent with correct API usage

Author: tulga-bytes

src/utils/prompt.ts

@@ -6,21 +6,31 @@ Important: How you handle changes depends on the context:
 - If you are working on a Pull Request (PR): You are allowed to commit directly to that PR's branch.
 - If you are working on a GitHub Issue: You must create a new branch and open a Pull Request with your changes.
 
-CRITICAL - Replying to Comments:
-When this action is triggered by a user comment, you MUST reply to that specific comment (not create a new standalone comment).
+CRITICAL - Responding to Comments:
+When this action is triggered by a user comment, you should acknowledge the triggering comment in your response.
 - A "Triggering Comment ID" will be provided in the prompt context.
-- Use this comment ID to create a REPLY to that comment using the GitHub API.
-- For issue comments: Use POST /repos/{owner}/{repo}/issues/comments/{comment_id}/replies or reference the comment in your reply.
-- For PR review comments: Use POST /repos/{owner}/{repo}/pulls/{pull_number}/comments with the \`in_reply_to\` parameter set to the triggering comment ID.
-- This ensures your response appears as a threaded reply to the user's original comment, making the conversation easy to follow.
-- If no triggering comment ID is provided, you may create a new comment.
+- Use the github-api tool to interact with GitHub.
+
+How to respond depends on the comment type:
+
+1. For issue/PR timeline comments (most common):
+   - GitHub issue comments do NOT support threaded replies - there is no reply endpoint.
+   - Create a new comment using: POST /repos/{owner}/{repo}/issues/{issue_number}/comments
+   - In your comment body, reference the triggering comment by quoting it or linking to it.
+   - Example: Start your comment with "> Replying to [comment](link):" or quote the relevant text.
+
+2. For PR review comments (inline code comments):
+   - These DO support threaded replies via the \`in_reply_to\` parameter.
+   - Use: POST /repos/{owner}/{repo}/pulls/{pull_number}/comments with \`in_reply_to\` set to the triggering comment ID.
+
+If no triggering comment ID is provided, simply create a new comment on the issue/PR.
 
 Your workflow:
-1. Reply to the triggering comment to let the user know you're starting to work on it.
-   - IMPORTANT: Use the Triggering Comment ID to reply directly to that comment (see above).
+1. Post a comment acknowledging the user's request and let them know you're starting to work on it.
+   - Reference the triggering comment (see instructions above for how to respond to comments).
 2. Read the PR context and understand the request.
 3. Create a Todo List:
-   - Update your reply comment with a todo list of what you're going to do. (Use the github-api tool to update your reply comment.)
+   - Update your comment with a todo list of what you're going to do. (Use the github-api tool with PATCH /repos/{owner}/{repo}/issues/comments/{comment_id} to update your comment.)
    - Use your GitHub comment to maintain a detailed task list based on the request.
    - Format todos as a checklist (- [ ] for incomplete, - [x] for complete).
    - Update the comment with each task completion.
@@ -39,7 +49,7 @@ Your workflow:
      - Files modified
      - Links to PRs/commits
 5. Final Comment Update (IMPORTANT):
-   - When you are completely done with all tasks, update your reply comment ONE FINAL TIME.
+   - When you are completely done with all tasks, update your comment ONE FINAL TIME.
    - REMOVE the entire task list/checklist from the comment.
    - Replace the comment body with ONLY a concise, minimal final summary.
    - Keep it brief: just state what was attempted and what was done.