Replace Date.now() with performance.now() for duration measurements (#258)

* Replace Date.now() with performance.now() for duration measurements

- Import performance from node:perf_hooks in all affected files
- Update Timer and ThinkingTimer classes to use performance.now()
- Update activity tracking (markActivity, getIdleMs) to use performance.now()
- Update cache duration measurements to use performance.now()
- Update agent execution timing (cursor, opencode) to use performance.now()
- Update subprocess execution timing to use performance.now()
- Update API performance monitoring to use performance.now()
- Update prep phase timing to use performance.now()
- Update timer.test.ts to mock performance.now() instead of Date.now()

Benefits:
- Monotonic clock immune to system clock adjustments
- Higher precision (microsecond vs millisecond resolution)
- Purpose-built for performance measurement

Fixes #245

* fix lint.

* Round float durations to integers in logging

Preserve original behavior by rounding performance.now() float values
to integers when displaying/logging millisecond durations.

* fix lint.

---------

Co-authored-by: pullfrog[bot] <226033991+pullfrog[bot]@users.noreply.github.com>
Co-authored-by: Robin Tail <robin_tail@me.com>

agents/opencode.ts

@@ -3,6 +3,7 @@
 // changes to web search configuration should be reflected in wiki/websearch.md
 import { mkdirSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
+import { performance } from "node:perf_hooks";
 import { ghPullfrogMcpName } from "../external.ts";
 import { getIdleMs, markActivity } from "../utils/activity.ts";
 import { log } from "../utils/cli.ts";
@@ -93,7 +94,7 @@ export const opencode = agent({
     log.debug(`» HOME: ${env.HOME}`);
     log.debug(`» XDG_CONFIG_HOME: ${env.XDG_CONFIG_HOME}`);
 
-    const startTime = Date.now();
+    const startTime = performance.now();
     let eventCount = 0;
     const thinkingTimer = new ThinkingTimer();
 
@@ -190,8 +191,10 @@ export const opencode = agent({
         },
       });
 
-      const duration = Date.now() - startTime;
-      log.info(`» OpenCode CLI completed in ${duration}ms with exit code ${result.exitCode}`);
+      const duration = performance.now() - startTime;
+      log.info(
+        `» OpenCode CLI completed in ${Math.round(duration)}ms with exit code ${result.exitCode}`
+      );
 
       // if zero events processed, something went wrong - surface stderr context
       if (eventCount === 0) {
@@ -243,7 +246,7 @@ export const opencode = agent({
       };
     } catch (error) {
       // activity timeout or process timeout - surface the real cause
-      const duration = Date.now() - startTime;
+      const duration = performance.now() - startTime;
       const errorMessage = error instanceof Error ? error.message : String(error);
       const isActivityTimeout = errorMessage.includes("activity timeout");
 
@@ -583,11 +586,11 @@ const messageHandlers = {
     if (toolId) {
       const toolStartTime = toolCallTimings.get(toolId);
       if (toolStartTime) {
-        const toolDuration = Date.now() - toolStartTime;
+        const toolDuration = performance.now() - toolStartTime;
         toolCallTimings.delete(toolId);
         const stepContext = currentStepId ? ` (step=${currentStepType || "unknown"})` : "";
         log.debug(
-          `» OpenCode tool_result${stepContext}: id=${toolId}, status=${status}, duration=${toolDuration}ms`
+          `» OpenCode tool_result${stepContext}: id=${toolId}, status=${status}, duration=${Math.round(toolDuration)}ms`
         );
         if (output) {
           log.debug(`  output: ${typeof output === "string" ? output : JSON.stringify(output)}`);