GitHub webhooks continuous deployment script no longer working. Possibly permissions issues?

I run a GitHub webhook continuous integration script that fetches the latest commit, runs a fresh Hugo build, and moves the new files into my sites public directory. (I manage my server with ServerPilot, if that matters.)

This works fine on 5 or the 6 sites I run, but sometime in the last month, this fails on one of my sites. Specifically, the build script now lacks permission to move files into the public directory for my app (the pull and build steps work fine).

As this only happens in one of my applications, I suspect there’s a permissions issue somewhere, and I’m not sure how to debug that or fix it. Any help would be much appreciated!

For context, here’s the deployment script.

<?php

	/**
	 * Automated deploy from GitHub
	 *
	 * https://developer.github.com/webhooks/
	 * Template from ServerPilot (https://serverpilot.io/community/articles/how-to-automatically-deploy-a-git-repo-from-bitbucket.html)
	 * Hash validation from Craig Blanchette (http://isometriks.com/verify-github-webhooks-with-php)
	 */

	// Variables
	$secret = getenv('GH_DEPLOY_SECRET');
	$repo_dir = '/srv/users/serverpilot/apps/gomakethings/build';
	$web_root_dir = '/srv/users/serverpilot/apps/gomakethings/public';
	$rendered_dir = '/public';
	$hugo_path = '/usr/local/bin/hugo';

	// Validate hook secret
	if ($secret !== NULL) {

		// Get signature
		$hub_signature = $_SERVER['HTTP_X_HUB_SIGNATURE'];

		// Make sure signature is provided
		if (!isset($hub_signature)) {
			file_put_contents('deploy.log', date('m/d/Y h:i:s a') . ' Error: HTTP header "X-Hub-Signature" is missing.' . "\n", FILE_APPEND);
			die('HTTP header "X-Hub-Signature" is missing.');
		} elseif (!extension_loaded('hash')) {
			file_put_contents('deploy.log', date('m/d/Y h:i:s a') . ' Error: Missing "hash" extension to check the secret code validity.' . "\n", FILE_APPEND);
			die('Missing "hash" extension to check the secret code validity.');
		}

		// Split signature into algorithm and hash
		list($algo, $hash) = explode('=', $hub_signature, 2);

		// Get payload
		$payload = file_get_contents('php://input');

		// Calculate hash based on payload and the secret
		$payload_hash = hash_hmac($algo, $payload, $secret);

		// Check if hashes are equivalent
		if (!hash_equals($hash, $payload_hash)) {
		    // Kill the script or do something else here.
		    file_put_contents('deploy.log', date('m/d/Y h:i:s a') . ' Error: Bad Secret' . "\n", FILE_APPEND);
		    die('Bad secret');
		}

	};

	// Parse data from GitHub hook payload
	$data = json_decode($_POST['payload']);

	$commit_message;
	if (empty($data->commits)){
		// When merging and pushing to GitHub, the commits array will be empty.
		// In this case there is no way to know what branch was pushed to, so we will do an update.
		$commit_message .= 'true';
	} else {
		foreach ($data->commits as $commit) {
			$commit_message .= $commit->message;
		}
	}

	if (!empty($commit_message)) {

		// Do a git checkout, run Hugo, and copy files to public directory
		exec('cd ' . $repo_dir . ' && git fetch --all && git reset --hard origin/master');
		exec('cd ' . $repo_dir . ' && ' . $hugo_path);
		exec('cd ' . $repo_dir . ' && cp -r ' . $repo_dir . $rendered_dir . '/. ' . $web_root_dir);

		// Log the deployment
		file_put_contents('deploy.log', date('m/d/Y h:i:s a') . " Deployed branch: " .  $branch . " Commit: " . $commit_message . "\n", FILE_APPEND);

	}