Upgrading and configuration files editing

I’m upgrading to 14.6 from my 14.2.1, where I extracted all configurations files from the WAR to /etc/xwiki.

Now I’m checking the configuration files for changes, and at first I’m check the stock configuration files (either from the Tomcat webapp directory or from GitHub e.g. xwiki.cfg) against my edited ones in /etc/xwiki.

But I’m stuck here, diff says my Hibernate file misses rows like:

> ## Note: This is starting the line in order not to put extra spaces when generated
> #foreach($mapping in $!xwikiDbHbmCommonExtraMappings.split(","))
>     <mapping resource="$mapping"/>
> #end
> ## Note: This is starting the line in order not to put extra spaces when generated
> #foreach($mapping in $!xwikiDbHbmPostgreSQLExtraMappings.split(","))
>     <mapping resource="$mapping"/>
> #end

where my file (in /etc/xwiki) has:

<     <mapping resource="instance.hbm.xml"/>
<     <mapping resource="notification-filter-preferences.hbm.xml"/>
<     <mapping resource="mailsender.oracle.hbm.xml"/>

Are those config files updated at runtime, beside my changes? Or am I using the wrong file from GitHub?

Another question: as I said, I copied the config files to /etc and edited them there, but it seems that even the config files inside the Tomcat webapps/ directory have been edited, is that expected?
Or maybe I copied them after a couple of restarts, can’t recall ATM.