dm: gpio: Rename set_dir_flags() method to update_flags()

The current method is a misnomer since it is also used (e.g. by stm32) to
update pull settings and open source/open drain.

Rename it and expand the documentation to cover a few more details.

Signed-off-by: Simon Glass <sjg@chromium.org>
Reviewed-by: Pratyush Yadav <p.yadav@ti.com>

Reviewed-by: Patrick Delaunay <patrick.delaunay@foss.st.com>