To speak to the second of naming things, I'm a big fan of content addressable everything. Addressing all content by hash_function(<the content>) has major advantages. This may require another naming layer to give human recognizable names to hashes, but I think this still goes a long way towards making things better.

You might find Joe Armstrong's The Mess We're In interesting, and provides some simple strawman algorithms for deduplication, though they probably aren't sophisticated enough to run in practice.

(My roomate walked in while I was watching that lecture when I had headphones on, and just saw the final conclusion slide:

• We've made a mess
• We need to reverse entropy
• Quantum mechanics sets limits to the ultimate speed of computation
• We need Math
• Abolish names and places
• Build the condenser
• Make low-power computers -- no net environmental damage

And just did that smile and nod thing. The above makes it sound like Armstrong is a crank, but it all makes sense in context, and I've deliberately copied just this last slide without any other context to try to get you to watch it. If you like theoretical computer science, I highly recommend watching the lecture.)