Fix all calls to htmlentities and htmlspecialchars, if you want to do ISO-8859-1 on PHP 5.4 or just be prepared.

fixstuff.php

#!/opt/local/bin/php
<?php
function getDirectoryList($dir, $skipExtensions = []) {
    $dirList = $fileList = [];

    if ($dfp = opendir($dir)) {
        while (($entry = readdir($dfp)) !== false) {
			$skip = false;
			foreach ($skipExtensions as $extension) {
				if (substr($entry, strlen($entry) - strlen($extension)) === $extension) {
					$skip = true;
				}
			}
			if (!$skip && $entry[0] != '.') {
				$path = "$dir/$entry";
				if (is_link($path)) {
				} else if (is_file($path)) {
					$fileList[] = $entry;
				} else if (is_dir($path)) {
					$dirList[$entry] = getDirectoryList($path, $skipExtensions);
				}
			}
        }
        closedir($dfp);

        uksort($dirList, 'strnatcmp');
        natsort($fileList);
    }

    return $dirList + $fileList;
}

function traverse($directoryList, $prepend = '') {
	foreach ($directoryList as $name => $entry) {
		if (is_array($entry)) {
			traverse($entry, $prepend . $name . '/');
		} else {
			doWork($prepend . $entry);
		}
	}
}

$htmlEntitiesPattern = '/(?:(?:htmlentities)|(?:htmlspecialchars))
	\(
		(
			(?:
				(?:
					\(
					[^\)\(]+
					\)
				)
				|
				(?:
					[^\)\(]+
				)
			)*
		)
	\)
/mx';

$paramsPattern = '/
	(?:,|^)\s*
	(
		(?:
			(?:[^\)\(,]+)?
			\(
			[^\)\(]+
			\)
		)
		|
		(?:
			[^\)\(,]+
		)
	)
/mx';

function doFixHtmlEntities($file) {
	global $htmlEntitiesPattern, $paramsPattern;

	if (($input = file_get_contents($file)) !== FALSE) {
		$matches = [];
		if (preg_match_all($htmlEntitiesPattern, $input, $matches, PREG_SET_ORDER)) {
			$res = '';
			foreach ($matches as $match) {
				$pMatches = [];
				preg_match_all($paramsPattern, $match[1], $pMatches, PREG_SET_ORDER);
				$args = [];
				while ($arg = array_shift($pMatches)) {
					$args[] = $arg[1];
				}
				$res .= 'func: ' . var_export($match[0], true) . "\n";
				$newArgs = [];
				if (isset($args[0])) {
					$newArgs[0] = array_shift($args);
					if (isset($args[0])) {
						$newArgs[] = array_shift($args);
					} else {
						$newArgs[] = 'ENT_COMPAT';
					}
					if (isset($args[0])) {
						$newArgs[] = array_shift($args);
					} else {
						$newArgs[] = "'ISO-8859-1'";
					}
					while ($nextArg = array_shift($args)) {
						$newArgs[] = $nextArg;
					}
					$newCall = str_replace($match[1], implode(', ', $newArgs), $match[0]);
					$res .= 'fixd: ' . var_export($newCall, true) . "\n";
					$input = str_replace($match[0], $newCall, $input);
					file_put_contents($file, $input);
				} else {
					$res .= "NO ARGS\n";
				}
			}
			//return var_export($matches, true);
			return $res;
		}
	} else {
		return 'ERROR: Could not read file.';
	}
}

function doWork($file) {
	if ($output = doFixHtmlEntities($file)) {
		echo $file . "\n";
		echo "$output\n";
	}
}

traverse(
	getDirectoryList('.', array('.swf', '.ini', '.xsl', '.png', '.jpg', '.yaml', '.yml', '.xml', '.json', '.txt', '.ico', '.sql', '.js', '.jar', '.java', '.css', '.gif', '.less'))
);