Since the latest update, I get the following warning messages when
starting applications from the terminal:

Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading
configurations from ~/.fonts.conf is deprecated.

I didn't find further documentation, what I should do about this:
Has this config file moved to another location (e.g. in ~/.config), is
it not supposed to be used at all anymore?
Would be good if there was a NEWS.Debian or some further information in
the warning message.

See also bug 1068549 on ubuntu, where there are suggestions
on a possibile patch to improve the wording on this warning.

https://bugs.launchpad.net/ubuntu/+source/fontconfig/+bug/1068549

The suggested fix, of moving ~/.fonts.conf to
~/.config/fontconfig/fonts.conf, has another problem: only newer
versions of fontconfig read that location, while older versions only
read ~/.fonts.conf .  That makes it impossible to have a single home
directory compatible with both old and new versions.  Suggested fix to
fontconfig: don't emit the warning if ~/.fonts.conf is a symlink to
~/.config/fontconfig/fonts.conf .

- Josh Triplett