From 9a3530fe66c64e34416380f8febcd3a4dd33aba0 Mon Sep 17 00:00:00 2001
From: Warren Wong <admin@wlmarketing.com>
Date: Wed, 12 Nov 2025 18:09:39 +0000
Subject: [PATCH] Fix directory structure: outputs/ for logs, runfiles/ for
 codex execution

---
 run.php | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/run.php b/run.php
index 450d1c3..a564521 100644
--- a/run.php
+++ b/run.php
@@ -27,8 +27,12 @@ if ($argc > 2 && is_numeric($argv[2])) {
     }
 }
 
-// NEW: Use runfiles subdirectory
-$baseOutputDir = 'runfiles';
+// NEW: Create runfiles subdirectory for codex execution
+$runfilesDir = 'runfiles';
+is_dir($runfilesDir) || mkdir($runfilesDir, 0777, true);
+
+// Outputs directory for logs and summaries (as before)
+$baseOutputDir = 'outputs';
 is_dir($baseOutputDir) || mkdir($baseOutputDir, 0777, true);
 $runIdentifier = date('Ymd_His');
 $runDir = sprintf('%s/run_%s', $baseOutputDir, $runIdentifier);
@@ -49,10 +53,15 @@ $logCli = function ($message, $channel = 'global') use (&$logFiles, $rawLogsDir)
     echo $message;
 };
 $logCli(sprintf("[%s] Run initialized in %s%s", date('Y-m-d H:i:s'), $runDir, PHP_EOL), 'startup');
+$logCli(sprintf("[%s] Codex execution directory: %s%s", date('Y-m-d H:i:s'), realpath($runfilesDir), PHP_EOL), 'startup');
 if ($startFrom > 1) {
     $logCli(sprintf("[%s] Starting from input line %d%s", date('Y-m-d H:i:s'), $startFrom, PHP_EOL), 'startup');
 }
-$runCommand = function ($command, $channel = 'global') use ($logCli) {
+$runCommand = function ($command, $channel = 'global') use ($logCli, $runfilesDir) {
+    // Change to runfiles directory for execution
+    $originalDir = getcwd();
+    chdir($runfilesDir);
+    
     $descriptorSpec = [
         0 => ['pipe', 'r'],
         1 => ['pipe', 'w'],
@@ -60,6 +69,7 @@ $runCommand = function ($command, $channel = 'global') use ($logCli) {
     ];
     $process = proc_open($command, $descriptorSpec, $pipes);
     if (!is_resource($process)) {
+        chdir($originalDir);
         $logCli(sprintf("Failed to start command: %s%s", $command, PHP_EOL), $channel);
         return ['', '', 1];
     }
@@ -126,6 +136,10 @@ $runCommand = function ($command, $channel = 'global') use ($logCli) {
     }
 
     $exitCode = proc_close($process);
+    
+    // Change back to original directory
+    chdir($originalDir);
+    
     return [$stdout, $stderr, $exitCode];
 };