changes to apply after upgrade (include system dir?)

[Peter Schober]

I thought files in /opt/shibboleth-idp/system/ are supposed to get
overwritten with newer versions when installing a new IDP version over
an older one?

I just noticed that 3.3.3 has this in ${idp.home}/system/conf/mvc-beans.xml:
  <import resource="conditional:${idp.home}/conf/mvc-beans.xml" />
but after upgrading my 3.3.2 to 3.3.3 my copy of that file still reads:
  <import resource="../../conf/mvc-beans.xml" />

Why does this matter: When one applies the changes to the config
directory from 3.3.2 to 3.3.3 the file ${idp.home}/conf/mvc-beans.xml
would get removed, but unless ${idp.home}/system/conf/mvc-beans.xml
would get changed accordingly this breaks the update.

What's the suggested process here? Not applying any updates to the
config directory at all? How would I know in advance that a change to
a file in config/ breaks the IDP unless another change to
system/config is also being made?

Apply changes to the system directory, too, on each upgrade (y'know,
the one with the file DONOTTOUCH in it)?

-peter