Describe the feature or problem you’d like to solve

The current MCP tools don't allow replying to existing pull request review comments. When a human reviewer leaves feedback, the available tools only support creating new top-level comments instead of responding within the existing comment thread.

Currently, the latest version of GitHub MCP server, doesn't allow this. AI leaves top level comments instead of responding to each comment under their respective threads.

Interestingly, this was possible with the older versions of the server, which seems to be introduced with #143 but later got lost during #410 (cc @williammartin).

Proposed solution

Please add a way to reply to individual threads just like what #143 did.

Example prompts or workflows (for tools/toolsets only)

I would like the establish a workflow as follows:

1. AI agent (e.g. claude code) creates a PR
2. I review and leave comments just like I am reviewing a teammates PR using the best and most familiar code reviewing interface of GitHub's.
3. I tell AI to fetch review comments, fix them and respond to each.
4. Iterative discussion continues within proper comment threads