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/gemini.ts

@@ -10,6 +10,7 @@ import { markActivity } from "../utils/activity.ts";
 import { log } from "../utils/cli.ts";
 import { installFromGithub } from "../utils/install.ts";
 import { spawn } from "../utils/subprocess.ts";
+import { ThinkingTimer } from "../utils/timer.ts";
 import { getGitHubInstallationToken } from "../utils/token.ts";
 import { type AgentRunContext, agent } from "./shared.ts";
 
@@ -112,17 +113,19 @@ const messageHandlers = {
       assistantMessageBuffer = "";
     }
   },
-  tool_use: (event: GeminiToolUseEvent) => {
+  tool_use: (event: GeminiToolUseEvent, thinkingTimer: ThinkingTimer) => {
     log.debug(JSON.stringify(event, null, 2));
     if (event.tool_name) {
+      thinkingTimer.markToolCall();
       log.toolCall({
         toolName: event.tool_name,
         input: event.parameters || {},
       });
     }
   },
-  tool_result: (event: GeminiToolResultEvent) => {
+  tool_result: (event: GeminiToolResultEvent, thinkingTimer: ThinkingTimer) => {
     log.debug(JSON.stringify(event, null, 2));
+    thinkingTimer.markToolResult();
     if (event.status === "error") {
       const errorMsg =
         typeof event.output === "string" ? event.output : JSON.stringify(event.output);
@@ -202,6 +205,7 @@ export const gemini = agent({
 
     let finalOutput = "";
     let stdoutBuffer = "";
+    const thinkingTimer = new ThinkingTimer();
 
     try {
       const result = await spawn({
@@ -230,7 +234,7 @@ export const gemini = agent({
               markActivity(); // reset activity timeout on every event
               const handler = messageHandlers[event.type as keyof typeof messageHandlers];
               if (handler) {
-                await handler(event as never);
+                await handler(event as never, thinkingTimer);
               }
             } catch {
               // ignore parse errors - might be non-JSON output from gemini cli