Basically is about to verify (with the code-checker?) that:

1) Recommend the use of make_(temp|cache|upload)_directory() when mkdir() calls are found.
2) Verify all calls to mkdir() are passing $CFG->directorypermissions
3) Each time a file is written, verify its permissions are being set. Basically check that after calling to fclose() or file_put_contents() there is a call to chmod() with the proper permissions.

Ciao