secure coding - How well does Checkmarx understand PHP and libraries?

Sorry for the very broad question but we have some problems, e.g. Checkmarx is complaining about code injection in something like the following

$accesskey = $_GET['accesskey'] ?? $argv[1] ?? null;
if (!$accesskey || !ctype_alnum($accesskey)) {
    throw new RuntimeException(sprintf('Passed accesskey "%s" is invalid', $accesskey));
}

$commandParts = ['echo', $accesskey]
$commandParts = array_map('escapeshellarg', $commandParts);
$command = implode(' ', $commandParts);
$command = escapeshellcmd($command);
system($command);

I think the commands are escaped and everything is fine but why is Checkmarx thinking different?

The application's <?php method calls an OS (shell) command with system, at line 1 of REDACTED, using an untrusted string with the command to execute.

This could allow an attacker to inject an arbitrary command, and enable a Command Injection attack.

The attacker may be able to inject the executed command via user input, _GET, which is retrieved by the application in the <?php method, at line 1 of REDACTED.

I'm also wondering if and how Checkmarx is able to understand library or framework code which is installed via Composer? E.g.

Assert::oneOf($unsafeUserInput, ['foo', 'bar']); // throws an Exception if $unsafeUserInput is not 'foo' or 'bar'
// $unsafeUserInput is now safe

or WP related stuff which is also often falsely flagged as being prone to SQL injections

global $wpdb;

$foo = $wpdb->getVar($wpdb->prepare('SELECT foo FROM bar WHERE baz = %s', $_GET['baz'] ?? ''));

If it checks for sanitisation methods is there a specific way they have to look? I honestly want to avoid changing too much code for Checkmarx.

Solution:

Your question of how well Checkmarx analyzes PHP code could lean towards a subjective answer and your perception of the tool can be biased given that you are using methods (escapeshellcmd) that are not recognized as sanitizers and the framework that you are inquiring about (Wordpress and Composer) are not technically supported.

In fairness to Checkmarx, they do support a variety of PHP frameworks such as Zend, Kohana, CakePHP, Symfony and Smarty which could end in lesser false positives (note: I'm not suggesting you switch platforms)

Any static analyzers would need some help from it users for it to be effective. I would advice you to exclude the Composer files from the scan.

You don't really don't have to make changes to the code and just argue with your AppSec team that these findings are false positives since the prepare method prevent SQL injection attacks and that escapeshellcmd does encode string. My recommendation however is to use escapeshellarg on $accesskey instead