I also wonder that you say you have certain apps built from sources against original Debian (Ubuntu uses those) packages, they are so old, most apps don't run against them (gui version problems with Gorm files, mostly).
Di dyou install perhaps Philippe's packages? or did a further mix?
No, I did not used Philippe's packages, but I have planned to do it.
I don't install from sources an application into the system, I don't know where it would end and especially if the bundle would be split up like the official ones do.
But sometimes you have no choices, when a binary package of the version you need does not exist
You could search for "appname". You should fins the binary inside the app bundle and you wil lprobaby find the shell script debian installs. Then quuery dpkg for the file ownership.
That's what I did. Now I have a clearer situation in mind!