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>

utils/setup.ts

@@ -120,8 +120,6 @@ export async function setupGit(params: SetupGitParams): Promise<void> {
   }
 
   // 2. setup authentication
-  log.info("» setting up git authentication...");
-
   // remove existing git auth headers that actions/checkout might have set
   try {
     execSync("git config --local --unset-all http.https://github.com/.extraheader", {
@@ -133,6 +131,29 @@ export async function setupGit(params: SetupGitParams): Promise<void> {
     log.debug("» no existing authentication headers to remove");
   }
 
+  // remove includeIf entries that actions/checkout@v6 uses for credential persistence.
+  // v6 stores credentials in an external file loaded via includeIf.gitdir, which our
+  // --unset-all above doesn't catch. without this, $git() would produce duplicate
+  // Authorization headers (one from includeIf, one from GIT_CONFIG_PARAMETERS).
+  try {
+    const configOutput = execSync("git config --local --get-regexp ^includeif\\.", {
+      cwd: repoDir,
+      encoding: "utf-8",
+      stdio: "pipe",
+    });
+    for (const line of configOutput.trim().split("\n")) {
+      const key = line.split(" ")[0];
+      if (!key) continue;
+      execSync(`git config --local --unset "${key}"`, {
+        cwd: repoDir,
+        stdio: "pipe",
+      });
+    }
+    log.info("» removed includeIf credential entries");
+  } catch {
+    log.debug("» no includeIf credential entries to remove");
+  }
+
   // SECURITY: set origin URL without token - auth is injected via GIT_CONFIG_PARAMETERS
   // in $git() calls. this prevents token leakage to git hooks and subprocesses.
   const originUrl = `https://github.com/${params.owner}/${params.name}.git`;