[Distutils] Persistent system-level files across installations

[Mac Ryan]

I am using stdeb to produce my debian packages and I am a novice when
it comes to packaging in general, so bear with me if I am mixing
together apples and oranges and just help me understanding better...

What I am trying to achieve is to have certain files of my application
that are persistent across software updates in other words: updating
from mypackage-1.0 to mypackage-1.0.1 should imply overwriting only
certain files of the v.1.0 if present, but not all of them. These
"persistent files" are application-specific and not user-specific (i.e.
they don't live in the /home/* hierarchy).

[If this information is of any use: said files are sqlite files with
usage statistic]

My questions:

At what level should I manage this? It is something I have to manage
within my application (1), within my setup.py configuration script (2),
or is something I am obliged to handle by dropping stdeb and packaging
for debian "from scratch" (3)? 

Any link to examples very much appreciated!

Thank you in advance for your time! :)

/mac