Re: Packaging Arbitrary Files
When asking questions it is a good idea to state what you are trying
to do up front rather than asking about a specific roadblock.
Packages that aren't in Debian can do whatever they want, including rm
-rf /usr/share/doc, deleting or modifying configuration files,
installing in /opt or whatever.
For apache2 use the conf.d and also take a look at how some PHP based
web applications approach this problem. Some examples that are based
on PHP in Debian include drupal, wordpress, phpmyadmin.
For proftpd, file a bug both in Debian and upstream asking for a
conf.d directory and add a patch if you want it to be fixed sooner.
Probably you should also be looking at systems like puppet, augeas &