feat(agents): add thinking time logging between tool calls (#244)

* feat(agents): add thinking time logging between tool calls

Adds a ThinkingTimer utility that tracks the gap between tool results and
the next tool call. When the gap exceeds 3 seconds, it logs the duration
with a stopwatch emoji (⏱️ 4.2s).

Uses performance.now() for high-resolution timing and Intl.NumberFormat
for rendering duration in seconds with optional fraction digits.

Integrated across all 5 agents: Claude, Codex, Cursor, Gemini, OpenCode.

Closes #127

* fix: adjusting tests for mocking performance.now.

* fix: reducing diff for claude.

* fix: rm unused args for claude.

* rm unused args for codex.

* fix: rm unused args for gemini.

* fix: rm unused args for opencode.

* mv THINKING_THRESHOLD.

* rev: I decided to pospone node:perf_hooks integration since it requires more comprehensive refactoring.

* fix: using Intl unit formatting.

* tests for ThinkingTimer.

* fix: narrow unit.

* fix: making durationFormatter a class instance property since using one agent per run.

* fix: inverting condition in markToolCall.

* thinking timer improvements and fix actions/checkout v6 auth

- thinking timer: use » chevron and "thought for X seconds" format
- thinking timer: add debug timestamps for sanity checking
- demote PID namespace isolation logs to debug
- remove redundant "setting up git authentication" log
- fix duplicate Authorization header with actions/checkout v6: clean up
  includeIf credential entries that v6 persists via external config files

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

* standardize tool call log prefix to » double chevron

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

* update timer tests for new thinking log format

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

---------

Co-authored-by: pullfrog[bot] <226033991+pullfrog[bot]@users.noreply.github.com>
Co-authored-by: Robin Tail <robin_tail@me.com>
Co-authored-by: Colin McDonnell <colinmcd94@gmail.com>
Co-authored-by: Cursor <cursoragent@cursor.com>

agents/cursor.ts

@@ -10,6 +10,7 @@ import { ghPullfrogMcpName } from "../external.ts";
 import { markActivity } from "../utils/activity.ts";
 import { log } from "../utils/cli.ts";
 import { installFromCurl } from "../utils/install.ts";
+import { ThinkingTimer } from "../utils/timer.ts";
 import { type AgentRunContext, agent } from "./shared.ts";
 
 // effort configuration for Cursor
@@ -144,6 +145,7 @@ export const cursor = agent({
     // track logged model_call_ids to avoid duplicates
     // cursor emits each assistant message twice: once without model_call_id, then again with it
     const loggedModelCallIds = new Set<string>();
+    const thinkingTimer = new ThinkingTimer();
 
     const messageHandlers = {
       system: (_event: CursorSystemEvent) => {
@@ -182,6 +184,7 @@ export const cursor = agent({
           const mcpToolCall = event.tool_call?.mcpToolCall;
           const builtinToolCall = (event.tool_call as any)?.builtinToolCall;
 
+          thinkingTimer.markToolCall();
           if (mcpToolCall?.args?.toolName && mcpToolCall?.args?.args) {
             log.toolCall({
               toolName: mcpToolCall.args.toolName,
@@ -194,6 +197,7 @@ export const cursor = agent({
             });
           }
         } else if (event.subtype === "completed") {
+          thinkingTimer.markToolResult();
           const result = event.tool_call?.mcpToolCall?.result?.success;
           const isError = result?.isError;
           if (isError) {