Also, what is the user function supposed to be used for? I tried looking in the manual and couldn't find anything. It's under shift+help.

It redefines keys. You make programs with the KEY function instead of the EXPORT function, and the function's name is K_ and then the key's name (numbers are themselves, but more complex key names use This Case). You then press User and then the key you redefined to execute the program. I know; at first, I was used to the 50g notion of adding functions to a userkey list and thus thought the key was useless; as it turns out, there's a different method for userkeys on the Prime.

Nope. That is a common convention, but really has nothing to do with the state of things...

Oh, that's good to know! Look at me here, always assuming the worst.

Examples please?

Eh, it's just a sort of an impression. Really, I'd be writing more about suggestions I have than things that are really missing. But, you did ask, so here goes:
* The app structure doesn't really have an HP calculator feel. Maybe if there was app 'folders' and/or an ability to hide apps?
* The "online" Help has a lot of typos, not to mention the accidental HP38gII syntax.
* Like the first point, there's no good way to organise your variables.
* There's no calculator-to-calculator linking. Even if the physical manual tries to claim there is ("Documentation which mentions sending data directly from one HP Prime to another should be disregarded" the sheet of paper that came with my Quick Start Guide says).
* All the undocumented CAS shortcut functions, described here. Some of them can cause crashes!
* Some basic apps we'd like are not here, like 3D graphing or periodic tables. No extra utility apps either.

All in all, it's a fine release, sure. But it just feels that much more limited than the HP calculators I'm used to (I mean heck, my 50g came with a built-in ARM assembler!). My hypothesis is that HP is just playing nice in the software until they get College Board approval, at which point I hope they'll add in more freedom to the OS. Of course, the College Board won't be easily convinced, so this could take a while to happen.

Here's just a raw dump of my Prime's data:

DATA: V0.025.5106    OS(1M):V0.025.5106
ADPT IN    :    BOOT ARMUboot V13
Samsung K9K2G08U0M    256 MB    SLC

So I see you've got the SDK version working! Have you found any differences in function yet?

EDIT: The HHC2013 is going on as we speak. I'm hoping some of our questions about native execution and the like will be answered there...

EDIT 2: I've been messing around with the file formats. The first byte of the custom app's .hpapp files seem to indicate what app it's copying.