I think your missing the point that 95+% of Pandora apps will not require any libraries, and thus any dependancies.
95% won't require any libraries? What kind of magic applications are these? Written totally from scratch, not using a single graphic library (be that qt, gtk, opengl, whatever)? Talk about bloatware. Presumably you are talking about game emulators or some such. In any case, I think you will find that on the Pandora 95% of the software will be totally normal software, i.e. they all use a lot of libraries, starting with libc.
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The only way zip files will be a mess on Pandora is if you try and save a couple of meg of space on your sd card because you want all the libraries seperate, rather than leaving them with the application, which can easily be fixed by static linking.
This is not at all about saving space on an SD card. I think you're missing the point completely. For example, if you just unpack a zip file, how are you supposed to remove that piece of software? Without a package manager? (And no, I don't think 'remove manually, file-by-file' is a good argument. That's messy on a desktop, that'll be messy on Pandora.)
The point about libraries is that I of course want every application which uses lib X to use _the same copy of lib X_. Exactly as what happens on any non-insane Linux installation everywhere. That way I can run e.g. a browser, a game, a mapping application, an email client at the same time, and there's still just a single copy in memory of the libraries they have in common.
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If every package is self-contained, this would mean that an application uses its own copy of every library it uses. (With the possible exception of 'core' libraries that are presumed to always be available somewhere on the NAND). That'll completely bloat the memory footprint of the applications.
That argument is becoming boring now, everyone states the same argument, completely ignoring the reasons why we don't think it's a good idea.
As you can see I made the same argument again, and I'm totally baffled as to why that would not be a good idea. The only time it wouldn't matter is if you want to run only a single program at a time, at all times. If that's so then I can't see why you would want something as powerful as the Pandora to begin with.