move instructions logging earlier and clarify built-in tool logs

Log the instructions box immediately after instruction resolution in main, and standardize agent permission summaries to debug-level "disallowed built-ins" output to reduce confusion with pullfrog MCP tools.

Co-authored-by: Cursor <cursoragent@cursor.com>

main.ts

@@ -167,6 +167,17 @@ export async function main(): Promise<MainResult> {
       repo: runContext.repo,
       modes,
     });
+    // log instructions as soon as they are fully resolved
+    const logParts = [
+      instructions.eventInstructions
+        ? `EVENT-LEVEL INSTRUCTIONS:\n${instructions.eventInstructions}`
+        : null,
+      instructions.user ? `USER REQUEST:\n${instructions.user}` : null,
+      instructions.event,
+    ].filter(Boolean);
+    log.box(logParts.join("\n\n---\n\n"), {
+      title: "Instructions",
+    });
 
     // run agent, optionally with timeout enforcement
     activityTimeout = createProcessOutputActivityTimeout({