docs: recommend not mixing manual tag mgmt with machine-tags.d/

We want to keep our options open for more automatic handling of
machine-tags in the future. So let's ask people to not use manual mgmt if
we detect that automatic mgmt is being used.

(The first version of this commit made hostnamectl emit a warning if any
machine-tags.d/ config was present. But this would mean that setting tags
through udev would cause warnings to be emitted. Let's just document the
general principle for now.)

man/machine-tags.d.xml

@@ -46,6 +46,10 @@
     stored in <filename>/etc/machine-info</filename>, thus applying the same configuration repeatedly has no
     further effect.</para>
 
+    <para>Note: when <filename>machine-tags.d/</filename> files are used, direct management of tags through
+    <command>hostnamectl tags …</command> or by editing the <filename>/etc/machine-info</filename> file
+    directly are <emphasis>not recommended</emphasis>. Please use one approach or the other.</para>
+
     <para>During boot, the configuration is applied automatically by
     <citerefentry><refentrytitle>systemd-machine-tags.service</refentrytitle><manvolnum>8</manvolnum></citerefentry>.</para>