Resolves #2448

What

Replaces add_reply_to_pull_request_comment with a consolidated pull_request_comment_write tool supporting three methods:

• reply — add a reply to an existing review comment (identical behavior to the old tool)
• update — replace the body of a review comment (PATCH /repos/{owner}/{repo}/pulls/comments/{comment_id})
• delete — delete a review comment (DELETE /repos/{owner}/{repo}/pulls/comments/{comment_id})

Why a consolidated tool instead of the two tools proposed in #2448

• Follows the established pattern of discussion_comment_write and pull_request_review_write (method-parameter write tools).
• Keeps the default tool count flat: one tool replaced by one tool, instead of net +2.
• add_reply_to_pull_request_comment is preserved via a deprecation alias per docs/tool-renaming.md, so existing --tools / X-MCP-Tools configurations keep working.

Use case (from #2448)

When an agent needs to correct or retract a review comment it previously posted, the only mutation available today is adding a new reply — leaving the stale original visible and creating thread noise. The workaround is gh api with PATCH/DELETE, bypassing the MCP server. With this change agents can clean up their own review comments programmatically.

Testing

• go test ./... — full suite passes
• UPDATE_TOOLSNAPS=true go test ./pkg/github/ — snapshot regenerated
• script/generate-docs — README + tool-renaming docs regenerated
• golangci-lint run (v2.9.0) — 0 issues
• 14 unit test cases: success paths for all three methods, required-parameter validation per method, and API error mapping (403 on updating another user's comment, 404 on deleting a non-existent comment)