Inconsistent gateway.xml deployment descriptors when topology contains application

Topologies with applications don't get gateway.xml updates on redeployment.

To reproduce, add an application to the admin.xml topology. For example

<application>
<name>admin-ui</name>
</application>

Then add a new provider, for example:

<provider>
<role>webappsec</role>
<name>WebAppSec</name>
<enabled>true</enabled>
<param>
<name>xframe.options.enabled</name>
<value>true</value>
</param>
<param>
<name>cors.enabled</name>
<value>true</value>
</param>
</provider>

The deployment now contains two gateway.xml files and only the gateway.xml file contains the WebAppSec related filters.