Patching $CERTI_SRC/CMakeLists.txt by moving a double quote and avoid…

…ing "clang: error: no such file or directory: ';-flat_namespace'". See https://savannah.nongnu.org/bugs/index.php?53964

Try pushing the nightly tag.

git clone command should only list the gh-pages branch. Updated how w…

…e copy javadoc and jsdoc output.