Currently, we only re-parse the top-level configuration file when it has
changed itself. This can cause problems when an include is changed, as
we were not updating all values correctly.

Instead of conditionally reparsing only refreshed files, the logic
becomes much clearer and easier to follow if we always re-parse the
top-level configuration file when either the file itself or one of its
included configuration files has changed on disk. This commit implements
this logic.

Note that this might impact performance in some cases, as we need to
re-read all configuration files whenever any of the included files
changed. It could increase performance to just re-parse include files
which have actually changed, but this would compromise maintainability
of the code without much gain. The only case where we will gain anything
is when we actually use includes and when only these includes are
updated, which will probably be quite an unusual scenario to actually be
worthwhile to optimize.