config: drop `git_config_set_in_file_gently()` wrapper

config: drop `git_config_set_in_file_gently()` wrapper

In 036876a1067 (config: hide functions using `the_repository` by
default, 2024-08-13) we have moved around a bunch of functions in the
config subsystem that depend on `the_repository`. Those function have
been converted into mere wrappers around their equivalent function that
takes in a repository as parameter, and the intent was that we'll
eventually remove those wrappers to make the dependency on the global
repository variable explicit at the callsite.

Follow through with that intent and remove
`git_config_set_in_file_gently()`. All callsites are adjusted so that
they use `repo_config_set_in_file_gently(the_repository, ...)` instead.
While some callsites might already have a repository available, this
mechanical conversion is the exact same as the current situation and
thus cannot cause any regression. Those sites should eventually be
cleaned up in a later patch series.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>