Fix codechecker issues.

deploy.php

questiontestrun.php

questiontype.php

replacedollars.php

replacedollarsindex.php

stack/answertest/at_general_cas.class.php

stack/answertest/tests/at_general_cas_test.php

stack/cas/casstring.class.php

stack/cas/tests/casstring_test.php

stack/input/algebraic/tests/algebraic_test.php

stack/mathsoutput/tests/mathsoutputmathjax_test.php

stack/mathsoutput/tests/mathsoutputmaths_test.php

stack/mathsoutput/tests/mathsoutputtex_test.php

stack/tests/potentialresponsenode_test.php

tests/walkthrough_adaptive_test.php

yui/input/input.js