that depends on how old your current version is.
f.i.
public/ => last change, 10 month ago
script/ => 9 months, except I added the ci-script you probably dont need
config/ => 6 months
If you do unit-tests you should update test/fixtures/config/config (3 months old)
then it's all of the above.
;-)
Generally just copy the folders from your framework-dir to your app-dir overwriting the old ones. (If you have patched some of those files, you have to be careful though. A version control system like git would be helpful then.)
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