Fix lots of codechecker issues.

db/upgrade.php

edit_stack_form.php

question.php

questiontestrun.php

stack/answertest/tests/at_general_cas_test.php

stack/cas/cassession.class.php

stack/cas/castext.class.php

stack/cas/connector.server.class.php

stack/cas/tests/casstring_test.php

stack/cas/tests/castext_test.php

stack/input/algebraic/tests/algebraic_test.php

stack/input/boolean/tests/boolean_test.php

stack/input/inputstate.class.php

stack/input/matrix/matrix.class.php

stack/input/matrix/tests/matrix_test.php

stack/input/tests/fixtures.class.php

stack/potentialresponsenode.class.php

stack/questiontest.php

stack/tests/options_test.php

tests/helper.php