I agree that the documentation is a bit lacking, but they can't on the other hand put together a 300 page document describing every bit and piece of the SDK. It would take too much time and a good programmer would be able to figure it out anyways by reading the code.
I think what we are indeed missing is a tutorial on file organisation. Valve has not said anything yet on how to deploy a MOD to a target user's machine. Do we create our own folder? Do we create a folder inside the hl2/ dir, how do we get the mod to show up in steam, etc...
As for the code, basically you have base classes (the regular named classes) and your own classes for your mod (usually have "SDK" in the name and are contained in file starting by sdk_). As omega said (either here or on wavelength, can't remember), basically you modify these files and add onto them to make your own mod. The HL2_DLL folder is to give you the example of an actual game done with the SDK, nothing more.
After that there's neat little pages like these : http://www.t-computers.co.uk/sniperumm/ that have popped up to help you. They basically turn the class hierarchy into a more human-readable format with graphs, etc... They can be helpful but they can also be confusing, it's up to each person to see wether it helps them or hinders their progression.
All i can say is i felt a bit like i did at first when i opened the HL1 SDK for the first time: confused!
Lots of files, lots of new names reffering to things unknown to me, etc... Knowing the HL1 SDK's naming scheme helped a lot, but there's still new stuff you need to learn, and especially the new class hierarchy and where your functions are. I find myself thinking alot like "Where did they put InstallGameRules in this thing" or "Hmm now they have a class for a sphere find instead of just a function..." . I say the best way is still to dig in, there's no head or tails to the SDK, just possible entry points. Start with gamerules maybe, or network code, or weapons, they're all good starting points :)
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