These are planning-ahead changes to make future upgrades smoother. See https://gist.github.com/2355445 for full reasoning.
The two changes in this pull are:
- Treat transactions with a version number greater than 1 as non-standard (don't mine or relay them).
- Warn the user (via the existing Qt/RPC GetWarnings() mechanism) if the blocks in the blockchain are a new version that this bitcoin doesn't understand.