I think the thing that does not want to be merged is installs and upgrades - people will end up upgrading when they don't want to.
if there was, for eg., a seperated "search for upgrades" link, then you could list all available upgrades - grouped by package. The repository could even offer multiple versions. Let's say we're in the year 2006 and someone has 5.0 installed, they would see half a dozen available upgrades, and they may want to only upgrade to version 5.2 for some reason.
for the install - good point. maybe the install from file system could even go into the developer admin page....
