scripts: update_sm32_package: Fix issue with common_ll directory

When running ./update_stm32_package.py, script breaks due to
unexpected presence of common_ll/ under stm32cube/ .
Skip update when this directory is parsed.

Additionally, update README to avoid recurrent issue when using
the script.

Signed-off-by: Erwan Gouriou <erwan.gouriou@linaro.org>