Fixed most issues from Moodle codechecker

classes/file_storage.php

classes/framework.php

classes/results.php

classes/task/look_for_updates.php

classes/task/remove_old_log_entries.php

classes/task/remove_tmpfiles.php

classes/upload_libraries_form.php

classes/user_grades.php

classes/xapi_result.php

db/install.php

db/upgrade.php

grade.php

index.php

lib.php

locallib.php

mod_form.php

review.php

settings.php