The vulnerability stems from a misconfiguration in the 'uploads/.htaccess' file, which failed to block .html file uploads. This allowed attackers to upload malicious HTML files leading to XSS. The core issue lies in server configuration (Apache directives in .htaccess) rather than specific PHP functions. While file upload handling functions might be involved indirectly, the provided data (commit diffs, CVE description) explicitly points to the .htaccess configuration as the root cause. No specific PHP functions in the codebase are identified with high confidence from the available information.