fix: issue properly basing diffs when tagged on pr

mcp/checkout.ts

@@ -490,7 +490,10 @@ export function CheckoutPrTool(ctx: ToolContext) {
         `use the TOC line ranges as your checklist and read specific files from the diff. ` +
         `for example, if the TOC says "src/foo.ts → lines 5-42", read lines 5-42 from diffPath. ` +
         `review files selectively based on relevance. ` +
-        `to inspect the PR's changed files, use diffPath — do NOT run git diff commands. ` +
+        `IMPORTANT: to inspect the PR's changed files, read diffPath directly — ` +
+        `do NOT run git diff or git show. The PR base branch is '${pr.baseRef}', NOT necessarily 'main' — ` +
+        `if you must use git, use 'origin/${pr.baseRef}' as the base (e.g. git log origin/${pr.baseRef}..HEAD), ` +
+        `but prefer diffPath for all diff analysis. ` +
         (incrementalDiffPath
           ? ` IMPORTANT: read incrementalDiffPath FIRST to understand what changed since last review, then use diffPath for full context.`
           : "") +