core: Always use runtime for gpgconf changes

* src/engine-gpgconf.c (gpgconf_write): Add --runtime.
* src/gpgme.h.in (gpgme_conf_opt_change): Document this
behavior.

If a tool uses GPGME for changing configuration values it
needs a way to ensure that these changes take effect. Otherwise
users may change and see config values and do not understand
why they are not working.