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/codex.ts

@@ -10,6 +10,7 @@ import { markActivity } from "../utils/activity.ts";
 import { log } from "../utils/cli.ts";
 import { installFromNpmTarball } from "../utils/install.ts";
 import { spawn } from "../utils/subprocess.ts";
+import { ThinkingTimer } from "../utils/timer.ts";
 import { type AgentRunContext, agent } from "./shared.ts";
 
 // configuration based on effort level
@@ -136,6 +137,7 @@ export const codex = agent({
 
     // Track command execution IDs to identify when command results come back
     const commandExecutionIds = new Set<string>();
+    const thinkingTimer = new ThinkingTimer();
 
     const env: NodeJS.ProcessEnv = {
       ...process.env,
@@ -170,7 +172,7 @@ export const codex = agent({
 
             const handler = messageHandlers[event.type as keyof typeof messageHandlers];
             if (handler) {
-              await handler(event as never, commandExecutionIds);
+              await handler(event as never, commandExecutionIds, thinkingTimer);
             }
           } catch {
             // ignore parse errors - might be non-JSON output
@@ -210,7 +212,8 @@ export const codex = agent({
 
 type ThreadEventHandler<type extends ThreadEvent["type"]> = (
   event: Extract<ThreadEvent, { type: type }>,
-  commandExecutionIds: Set<string>
+  commandExecutionIds: Set<string>,
+  thinkingTimer: ThinkingTimer
 ) => void | Promise<void>;
 
 const messageHandlers: {
@@ -239,10 +242,11 @@ const messageHandlers: {
   "turn.failed": (event) => {
     log.error(`Turn failed: ${event.error.message}`);
   },
-  "item.started": (event, commandExecutionIds) => {
+  "item.started": (event, commandExecutionIds, thinkingTimer) => {
     const item = event.item;
     if (item.type === "command_execution") {
       commandExecutionIds.add(item.id);
+      thinkingTimer.markToolCall();
       log.toolCall({
         toolName: item.command,
         input: (item as any).args || {},
@@ -250,6 +254,7 @@ const messageHandlers: {
     } else if (item.type === "agent_message") {
       // Will be handled on completion
     } else if (item.type === "mcp_tool_call") {
+      thinkingTimer.markToolCall();
       log.toolCall({
         toolName: item.tool,
         input: {
@@ -268,13 +273,14 @@ const messageHandlers: {
       }
     }
   },
-  "item.completed": (event, commandExecutionIds) => {
+  "item.completed": (event, commandExecutionIds, thinkingTimer) => {
     const item = event.item;
     if (item.type === "agent_message") {
       log.box(item.text.trim(), { title: "Codex" });
     } else if (item.type === "command_execution") {
       const isTracked = commandExecutionIds.has(item.id);
       if (isTracked) {
+        thinkingTimer.markToolResult();
         log.startGroup(`bash output`);
         if (item.status === "failed" || (item.exit_code !== undefined && item.exit_code !== 0)) {
           log.warning(item.aggregated_output || "Command failed");
@@ -285,6 +291,7 @@ const messageHandlers: {
         commandExecutionIds.delete(item.id);
       }
     } else if (item.type === "mcp_tool_call") {
+      thinkingTimer.markToolResult();
       if (item.status === "failed" && item.error) {
         log.warning(`MCP tool call failed: ${item.error.message}`);
       } else if ((item as any).output) {