Add retrying. Improve diff format

mcp/checkout.ts

@@ -1,12 +1,85 @@
 import { writeFileSync } from "node:fs";
 import { join } from "node:path";
-import type { Octokit } from "@octokit/rest";
+import type { Octokit, RestEndpointMethodTypes } from "@octokit/rest";
 import { type } from "arktype";
 import type { ToolContext } from "../main.ts";
 import { log } from "../utils/cli.ts";
 import { $ } from "../utils/shell.ts";
 import { execute, tool } from "./shared.ts";
 
+type PullFile = RestEndpointMethodTypes["pulls"]["listFiles"]["response"]["data"][number];
+
+/**
+ * formats PR files with explicit line numbers for each code line.
+ * preserves all original diff info (file headers, hunk headers) and adds:
+ * OLD | NEW | TYPE | code
+ */
+export function formatFilesWithLineNumbers(files: PullFile[]): string {
+  const output: string[] = [];
+
+  for (const file of files) {
+    // file header
+    output.push(`diff --git a/${file.filename} b/${file.filename}`);
+    output.push(`--- a/${file.filename}`);
+    output.push(`+++ b/${file.filename}`);
+
+    if (!file.patch) {
+      output.push("(binary file or no changes)");
+      output.push("");
+      continue;
+    }
+
+    // parse and format the patch with line numbers
+    const lines = file.patch.split("\n");
+    let oldLine = 0;
+    let newLine = 0;
+
+    for (const line of lines) {
+      // hunk header: @@ -OLD,COUNT +NEW,COUNT @@ optional context
+      const hunkMatch = line.match(/^@@ -(\d+)(?:,\d+)? \+(\d+)(?:,\d+)? @@/);
+      if (hunkMatch) {
+        oldLine = parseInt(hunkMatch[1], 10);
+        newLine = parseInt(hunkMatch[2], 10);
+        output.push(line); // pass through unchanged
+        continue;
+      }
+
+      // code lines within hunks
+      const changeType = line[0] || " ";
+      const code = line.slice(1);
+
+      if (changeType === "-") {
+        // removed line: show old line number, no new line number
+        output.push(`${padNum(oldLine)} |     | - | ${code}`);
+        oldLine++;
+      } else if (changeType === "+") {
+        // added line: no old line number, show new line number
+        output.push(`    | ${padNum(newLine)} | + | ${code}`);
+        newLine++;
+      } else if (changeType === " " || changeType === "\\") {
+        // context line or "\ No newline at end of file"
+        if (changeType === "\\") {
+          output.push(line); // pass through as-is
+        } else {
+          output.push(`${padNum(oldLine)} | ${padNum(newLine)} |   | ${code}`);
+          oldLine++;
+          newLine++;
+        }
+      } else {
+        // unknown line type, pass through
+        output.push(line);
+      }
+    }
+    output.push(""); // blank line between files
+  }
+
+  return output.join("\n");
+}
+
+function padNum(n: number): string {
+  return n.toString().padStart(4, " ");
+}
+
 export const CheckoutPr = type({
   pull_number: type.number.describe("the pull request number to checkout"),
 });
@@ -170,16 +243,16 @@ export function CheckoutPrTool(ctx: ToolContext) {
         throw new Error(`PR #${pull_number} source repository was deleted`);
       }
 
-      // fetch PR diff via API (authoritative source - not affected by main advancing)
-      const diffResponse = await ctx.octokit.rest.pulls.get({
+      // fetch PR files and format with line numbers
+      const filesResponse = await ctx.octokit.rest.pulls.listFiles({
         owner: ctx.owner,
         repo: ctx.name,
         pull_number,
-        mediaType: { format: "diff" },
+        per_page: 100,
       });
-
-      // write diff to file for grep access
-      const diffContent = diffResponse.data as unknown as string;
+      const diffContent = formatFilesWithLineNumbers(filesResponse.data);
+      const diffPreview = diffContent.split("\n").slice(0, 100).join("\n");
+      log.debug(`formatted diff preview (first 100 lines):\n${diffPreview}`);
       const tempDir = process.env.PULLFROG_TEMP_DIR;
       if (!tempDir) {
         throw new Error(

mcp/pr.ts

@@ -29,7 +29,7 @@ function buildPrBodyWithFooter(ctx: ToolContext, body: string): string {
   return `${bodyWithoutFooter}${footer}`;
 }
 
-export function PullRequestTool(ctx: ToolContext) {
+export function CreatePullRequestTool(ctx: ToolContext) {
   return tool({
     name: "create_pull_request",
     description: "Create a pull request from the current branch",

mcp/review.ts

@@ -11,7 +11,7 @@ export const CreatePullRequestReview = type({
   pull_number: type.number.describe("The pull request number to review"),
   body: type.string
     .describe(
-      "1-2 sentence high-level summary ONLY. Include urgency level and critical callouts (e.g., API key leak). ALL specific feedback MUST go in 'comments' array instead."
+      "1-2 sentence high-level summary with urgency level, critical callouts, and feedback about code outside the diff. Specific feedback on diff lines goes in 'comments' array."
     )
     .optional(),
   commit_id: type.string
@@ -20,12 +20,12 @@ export const CreatePullRequestReview = type({
   comments: type({
     path: type.string.describe("The file path to comment on (relative to repo root)"),
     line: type.number.describe(
-      "The line number in the file (use line numbers from the diff - usually the RIGHT side/new code)"
+      "Line number from the diff. Each code line shows 'OLD | NEW | TYPE | code'. Use NEW (second column) for added/context lines, OLD (first column) for removed lines."
     ),
     side: type
       .enumerated("LEFT", "RIGHT")
       .describe(
-        "Side of the diff: LEFT (old code) or RIGHT (new code). Defaults to RIGHT if not provided."
+        "Side of the diff: LEFT (old code, lines starting with -) or RIGHT (new code, lines starting with + or unchanged). Defaults to RIGHT."
       )
       .optional(),
     body: type.string.describe(
@@ -37,8 +37,7 @@ export const CreatePullRequestReview = type({
   })
     .array()
     .describe(
-      // FORK PR NOTE: checkout_pr returns the diff via GitHub API - use that for line numbers
-      "PRIMARY location for ALL feedback. 95%+ of review content should be here. Use the diff returned from checkout_pr to find correct line numbers (RIGHT side for new code, LEFT for old)."
+      "Inline comments on lines within diff hunks. Feedback about code outside the diff goes in 'body' instead."
     )
     .optional(),
 });

mcp/server.ts

@@ -24,7 +24,7 @@ import { GetIssueCommentsTool } from "./issueComments.ts";
 import { GetIssueEventsTool } from "./issueEvents.ts";
 import { IssueInfoTool } from "./issueInfo.ts";
 import { AddLabelsTool } from "./labels.ts";
-import { PullRequestTool } from "./pr.ts";
+import { CreatePullRequestTool } from "./pr.ts";
 import { PullRequestInfoTool } from "./prInfo.ts";
 import { CreatePullRequestReviewTool } from "./review.ts";
 import { GetReviewCommentsTool, ListPullRequestReviewsTool } from "./reviewComments.ts";
@@ -83,7 +83,7 @@ export async function startMcpHttpServer(
     IssueInfoTool(ctx),
     GetIssueCommentsTool(ctx),
     GetIssueEventsTool(ctx),
-    PullRequestTool(ctx),
+    CreatePullRequestTool(ctx),
     CreatePullRequestReviewTool(ctx),
     PullRequestInfoTool(ctx),
     CheckoutPrTool(ctx),