run_ci.sh: Fix setting of twister_exclude_tag_opt

We were testing modified_tags.args before we called get_twister_opt.py
so it would never have been created and thus twister_exclude_tag_opt
would never get set correctly.  Move the check to after we call
get_twister_opt.py

Also we need to remove modified_tags.args once we are done with it.

Signed-off-by: Kumar Gala <kumar.gala@linaro.org>