chore: add a comment in bin/emqx to warn the config overlay

bin/emqx

@@ -342,6 +342,9 @@ generate_config() {
     NOW_TIME="$(call_hocon now_time)"
 
     ## ths command populates two files: app.<time>.config and vm.<time>.args
+    ## NOTE: the generate command merges environment variables to the base config (emqx.conf),
+    ## but does not include the cluster-override.conf and local-override.conf
+    ## meaning, certain overrides will not be mapped to app.<time>.config file
     ## disable SC2086 to allow EMQX_LICENSE_CONF_OPTION to split
     # shellcheck disable=SC2086
     call_hocon -v -t "$NOW_TIME" -I "$CONFIGS_DIR/" -s $SCHEMA_MOD -c "$RUNNER_ETC_DIR"/emqx.conf $EMQX_LICENSE_CONF_OPTION -d "$RUNNER_DATA_DIR"/configs generate