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>

agents/gemini.ts

@@ -413,7 +413,7 @@ function configureGeminiSettings(ctx: AgentRunContext): string {
   writeFileSync(settingsPath, JSON.stringify(newSettings, null, 2), "utf-8");
   log.info(`» Gemini settings written to ${settingsPath}`);
   if (exclude.length > 0) {
-    log.info(`» excluded tools: ${exclude.join(", ")}`);
+    log.debug(`» disallowed built-ins: ${JSON.stringify(exclude)}`);
   }
 
   return model;