Deprecate `update` subcommand; introduce `apply`

This commit is a follow-up to the discussion in the ksonnet.next design
doc, in which users consistently expressed their preference that the
`update` command be called `apply`.

NOTE: We have renamed `pkg/kubecfg/update_test.go` ->
`pkg/kubecfg/apply_test.go`, but we copy the `update`'s integration test
file. The reason is that the `update` unit tests actually test things
like GC (rather than the command itself), so the file name is
inconsequential. On the other hand, the integration tests test the
commands themselves, so it is important to have two copies, one for
`update` and one for `apply`.