First of all, very nice work! It seems to be already usable and useful, therefore I made a (small) well deserved donation to the bounty! - the bounty is still open for donors - hint! hint!

I'd have a couple of suggestions:
- I think the client should report an up-to-date packet if the only diffs are located in the icons: for instance, you get an orange sign if you change a tooltype, and this would happen if you changed the icon with one taken from the Contrib/ dir often found in the archives. Of course you can easily check everything from MuCl, but I'd like the check to report the green signs in these cases, so that I don't have to further control.
- is it possible to have the possibility to create a packet and a description, save it in some kind of Packet Manager Description file, and then create/update an index (.pmi) just adding new "descriptions" (say, .pmd or anything else)? This would be useful for sites like MorphZone or morphos-news, and possibly AmiNet, if it was easy it wouldn't give much work to the moderators (even better if it was semi-automatic), and with just a couple of Index we would check the majority of software. Moreover, not all the authors would need some webspace of their own to support MorphUp. Yet, by adding the "description" themselves, there wouldn't be a duplication which would be confusing: all the sites would use that one. Moreover MuCl might cross check packages on different sources to get the latest, even if sometimes not all the sites have an updated one.
- this is more a question: if the user has a newer system file than the one that's going to be installed, is copy skipped by default?
- is it possible to create some cross-dependencies between packets? For instance, YAM needs some MUI classes not included in the archive: I think they should be "linked" (and downloaded with YAM itself anytime they are needed and not present/obsolete).
- I agree with the suggestion to let some scripting be executed as part of the installation process (even just simple DOS scripts). This should be carefully planned though, in order to prevent malicious exploits (although any unverified script is potentially dangerous).
- I would add some subclasses to the Package Classes: I have subdirs in Graphics and Games, for instance... It should be possible to discriminate between Picture Viewers/Image Processors/Paint Programs and 3D, or between SDL ports/Arcade/FPS, or between Browsers/P2P/Mail/Instant Messaging. In order not to give too much hassle to the user, uspecified subclasses should "backfall" to their principal class, so, if you have a single level tree you wouldn't need to specify anything more than now. In my case, a check for ShowGirls would fail as it stands now...

That's all, for now . I'd like to hear also Dr.Morbius and tokai opinion about this program, since they wrote a good article about Installation Procedures...

Kind regards,
Andrea